From ab3df6f7b7de255b3f816273e19c4ea086e638d7 Mon Sep 17 00:00:00 2001
From: niklasmueboe <muellni@pmn-bih-dh-12.charite.de>
Date: Sun, 19 Sep 2021 16:20:47 +0200
Subject: [PATCH 1/2] #22 further improvements on documentation

---
 docs/build/html/.doctrees/environment.pickle  | Bin 21627 -> 20993 bytes
 docs/build/html/.doctrees/index.doctree       | Bin 9531 -> 10323 bytes
 .../build/html/.doctrees/installation.doctree | Bin 11147 -> 10829 bytes
 docs/build/html/.doctrees/usage.doctree       | Bin 30364 -> 31780 bytes
 docs/build/html/_sources/index.rst.txt        |   9 +-
 docs/build/html/_sources/installation.rst.txt |  13 +-
 docs/build/html/_sources/usage.rst.txt        |  60 +++++-----
 docs/build/html/genindex.html                 |   1 -
 docs/build/html/index.html                    |   8 +-
 docs/build/html/installation.html             |  23 ++--
 docs/build/html/objects.inv                   |   5 +-
 docs/build/html/search.html                   |   1 -
 docs/build/html/searchindex.js                |   2 +-
 docs/build/html/tutorial.html                 | 111 ------------------
 docs/build/html/usage.html                    |  90 +++++++-------
 docs/source/index.rst                         |   9 +-
 docs/source/installation.rst                  |  13 +-
 docs/source/tutorial.rst                      |  10 --
 docs/source/usage.rst                         |  60 +++++-----
 19 files changed, 158 insertions(+), 257 deletions(-)
 delete mode 100644 docs/build/html/tutorial.html
 delete mode 100644 docs/source/tutorial.rst

diff --git a/docs/build/html/.doctrees/environment.pickle b/docs/build/html/.doctrees/environment.pickle
index 0615eff71d282aa88b76195fd17986ffde174100..33ad2a269d96f252d84e37c427f6ca410e6ba78e 100644
GIT binary patch
literal 20993
zcmcg!Ym6nwRrb#N{oGye!%41pNHR`5Gk%4b1QM^kUK3__y!O~aDBd)E@9mlHp1$38
z`!TbV#33Pyy(6_03%3yg#LomF@dqg(5DSn3B49z{m_UL8iU<-vkjz6NL7+%{=bWnU
zzK_Yyy?8S}rf=7&I(6#QdDW?^{`l}q-+$sZ{!164rtSFGS1o_n2?M`j`Ei!cJ)AgR
z{n1j<i`iYD$ezuX(?PS@%r?@AdQgi)%c?tJmfo{w2MuejkyxJRJ8My7HZD1_wT3#;
zT9r_(*>S^LTUCvsEFFo$8n-?7quNG664or#t_A*<vz?{Widy|X@`wO(^2UQ*D-4~w
z6@l7xII`k|$+fP>mLEBRA7xjwbhH@;u2sWG$2T|6UtaM*Eq>R6=6>jG+bF;9zI*Pw
z_wLGuv*Vdj<?@$b_B<<GdHBm;h-0T_TVciYqspdjM)sZ=S2j)C+y|Lv659b7a(8d-
zMnlW9%m^e5-m`jdmd?ahqv@Hk6&X!4wu#~iBQML$bk4e7^OCwn;MfXfP!q&sBetyu
z5X}jrj4-a}MGTK(6C=p+jv7(`q%&4CsT#E?GPWEK{6nuZ+@z&wnv2|0rD>TZBTBZm
zoa<RSSqs3dTFlH&Cm#>%R%q2PIAAxX>B%e|S`8x-ve1g+Fsa1}z%eE$i_&R7X<(v_
ztsrceF$>&iB)GtXP5D)MD+v&)p&{n-qO-lqMZ>XK^-wbQ6g|0Uq88Mxm8uuicF_Kk
z6UC0dO^_r#&I4&$=*V;Yoyc$?RG5K(`{XBpeb@97mZ4?)gncp{gnDEf&u8{&`;7fC
zex&nCgp88V+=j6cR<3!weae1}YK}r8N%AuLA~&_q+II+!;W(&6Zd7?X&acK+BhEIY
z!kB0J+ljet>4Hg&#Plo!sw09d?@?w-gHys4L$~9p^i7h8lOG9#AbxiBBO3PXN5J!E
zGif-{Fe6Bk0S$%PIDXx_t{`L7jLYp0a$S4HzE>K}s+qTZuo;Yn3MKK@%7ZHrbXDqB
z>^r6IRNdM#6E8Nx0CS|qcgn2SjjhCIVS!ABus*gGf$=w_)f`o51oZ@CreWlOH^rgT
zfS3faAH<dsT3Zk@zh)Ux(}cx1P@P70uxE%?M!ImOxxY<jE`sRqGc7z#3pO<0Bkj+*
zhq+T!D_+bOb%Le{xMHCFCi~4Y-LqOzjVkOAPaWf*-m$Evv1f)pIF%DKA0^Eu6d@`g
zS5;>xF>am+h*+Z$_y+2cf&tD5C!j@!)pWdITl15PAeg111!fc(UTB-K<(cSPF?Xg3
z9-84kCbwZako|!sgps9t%7<wOgV;A@8yh6Yb5d5aq|X8Zz*NKZn-J2-NJ7ZIU>NhA
zxarh(_Ok=7G^5@PXWI{;w^ya@@z!EY<TfNv0Y}6d=!siY#sLNazl^%ogl$|u#{Jn3
z*zb~#XJI&O0~M+eXVdd^>v=A>u7Qc#yeLv9bqgqu=FLRxMFtet+1l4dlT=iLbcJ!G
zM>&y1)XO$`O^q!APvdI|#4_jfLaEF!S=wP~u3fMcyN{RQ%C?gOTTaKdwz9epxF!ts
z7`s#$74QiT8Qh26VFPL<!h>lx<yE*8)_wb=%oCStYxLMdV=4p~qH?lX=>*ph7h=C`
zzf5HdMVV0&dWNa`P7F1&PfGnsuCF{HtR+_zg7jD*X%@^OL&WQV0MCiwS2Nv0d86DT
z!<usaSw;^B@5j!Tg9hnn;_vvuo<=DBM{v@xdiGbP)fl%*oH~`TgbV343Kz1w%0=6#
zW$7YCU1;S#Q3)C2YX+oJ%2_hNe!IOaJqp{jpKhs?3OC}QrbKv9kP78gjF?5~XkImf
zpTT&pmHUS^FrdNEJT2tMnXZPZ%8fmzPC9a%w35-VO@yYB6Loy}KA<g41ti)K`+q}<
z=NKm<s#@r<(aX6i5V%d)m}(Lu^3nXB=QewxL;jWwI2_OfLL=wHsBC)Dp?%I?QZ|!)
zG0UBfOa!n{0+fVL?4Q6`_|mg^99KaIRe`-r$i^eqA;-)0=eRybAI3&}<W>?@wRnng
zMg$uhK<63t6qjt7yBtGEp?#PA4u;zAwC|Q5KViRB>d$h0SklmJ9q$Q24PR^|%{n4L
zxJM2LxEqPRBFJaeg!aSraIrLkrv$eH-}HczL_&iX8K>BInpvmDhKZXBjGSx{2xaMU
z6=iEXvq~7Ubdh33L{>1;&Cm#{96@vBT^>~l(G3~)`|S5i1qmn10>(tBiD@DVSCV%i
z^#woymZ4Sxf>Fh8EXV?&2o5U4=uYx@i}E}$9a@bMWJ)C&IFSOi@*~R(Yc>U9C4xw2
zbz3#hLJ)P<1`u>iP!SI*dUCnj)BaQeL~2NVDEQUWC2?tx#LWcmJ&&x0IkHmJi&`Ko
zK(K>w1z|0@8m3)@L0lwxKpmA2tX5QG=|F~DggR=3Y9P#yvbks6(yeL<gA|gzzR12s
zF`a_by4WO;Rm_PDl^ha<2%67#@JvyN&JjAbu>3&BW%lbbBI%WVG(tRDOoZCkGTH|W
zvNI@DQiE_Lwq2M&UOT1lwd1%My=QH$R`*xksBU@AZn)}O@tWUktf{&W-M?l<?^?q|
ztTY<lN{t9ZWyLWLDF|b`37XMeDLYF3c;K03__t^7$}Ay2Z(MgGEb8{zX%9T}L8^3B
zSIQAV8nzIHsM*kM??VXKt^EG>@@)(2!Rs+aj3gS_jdWBMv45Y_a9TF7X}sY!j@@<}
z`S~dgOUO+g<mC&x94<XD*d%D@bS4KCwkI}2lu~FSKIe8_2kU6q-4N?$tZZqKeEQ<k
zmo8N{&R>4C^3#uAKL3GB51qeo;mJogH{X}#ou4RL%R&gtV6y=Wb?N-ZV^5!d3{5Xx
zddPEDgK)dlY>F1o*P%Vz<lWM-W*vbqN+jl-6{z+R97fq6L~a3j3r+>BQq`8!K#vRh
z5yWH(++3WQtQ`~5qqqz%nUfMEQy|i8kyXrlRsdv~<W~cWCb$(ZY4|FXR`gSq>#*lK
z!agna<DltTyOw9Dbu+EYB!E9I71})k)1z>fVuJx6?u`UvQJOJ`JPQJ7#2XBn5fHK$
zyr6;&<KmN2T=Gad{$cQ>fF;aypCkDz^&?S0p=k_L>}rV+7@#P?T-G39<n&a17$1ay
zwVk&0##ypT0>IiJ*n_n~_Q45}S;!mDl<FX%qgNxRi{j9_hU`FW*p>-<lsB9&*Fa1J
zKf8X6=_x^Cr(wamt2rqF_JVMSkgX55H!=Mhq86BV2AnE-QGjBM>A;8XR5Eu*Q7we*
z!?-r!Uv=+~Jrw>4hyRRn9P+B72ADAD!g#I=$hozIR;1Wx%=Kehw5O?QAvPixXQ;4Y
z?!bRa%7zja_!Wd&SQjJ6rDut&)&Y%s0<s`ha~>+__*(%b9ypTIT3VtED~>bnH_#+~
z%j3RP!Fa7oDNL;dTa`S|H+|WOYDiC-KA0cnin*Y>=~Toy4eF3?4d|*!IpGCQ(lMQ<
z5aB$b5%?IM6`PI+?MakMQTtf4t!7i4myW*UXI4IT?w!A=OzJdO@vS`?F~CEKkF<c8
z+eL;^K$nLA`6`t9Wz=eM+!7kdqUbs@h)6TUalY!Etr<?;K$?+5d~~M``vN5q;gGw*
z=4uAILU6ld?L(~VJbCFT5^dYQNdw|v!4_z*1_46LQF2%wTU}bvI6l%6u-lX=Kzb1C
z+i6Kt8qjg9zu~Q7JB0EXod1FsW%6fgwBSd^2SYG+@7If>Q#DSm7)YULomUmqBJ1{A
zvni2hXR3t}&vS*YY&cG!AHfJf5#A)*pfuRQy6yl06B$)%CIA)`%B5@AX{1G+rhz1y
zZ&Gs9sG7AMc+JSxBf7J>k3_R?kPArsYj8ER7OordepBbkR0iw>1RH8*c}=)(zpm0~
zSgfbxIfO%l#r#!QL=>>$o*j_r;CKP9Tf3B|p@mgCZ22otr@Y#!qMGVXryJ5^_ZHP=
zifXcA$`O?M*{Nb4k@}-FePM%EC_|oCpDPfdI;Wp<SP4~VH7HBi3ctN*D`_@uW)E@{
zr;92L$4BfDHVh9@1)M^`niA(CIA4)>`ztw;5{;6r%}T)8q6f7mohi)i&tlq&v7Rle
zQpil=0o9~D2(+~zr!)n5HA(wjEpVMIaPio&P>^VOb}fm*wW{N<*-jEWUeTn)t{ktl
zna|s3K+&pFbcFbqSC6m^*s{PfHHPXVk|-Dj$r4E|5?7Rg<w6$HdGZ&nRnn>4Rl!xz
zas=ANOB}A(Wf4~Z$wTS|l8(5qA;utODM%29G^YTZh2|WyYB8k%63(Q<K9=CSdZ|^0
zwXYtMq?%4kT+f>@(4+NZFbo{&s}eDz7*#rgm<~B>Y`qnmS2Jpzo_o2`D{5aW-w)IK
zZ1y;%?b9*vNb=~P#!_YCT7nEMEGt=5mGn<%BBYOvU97^akdkBRa1tTvgUNM#RD}!W
zg~JP=KHu4(Or_d!!X6(blcUvIwmy)aQWWNeHa0Yn;E!pjx3>cwm9GIzZ%gJ4vFo@#
zlxHS%F$*u@I^BlLHFr%(SP>bEZBSaaQTd6saxtsf`d~-@v}1(^?PNu9or*^UPqzLb
z_LY>yqr?~HQj#*+LAuaVj^!DW;0F+IVHX0|bPRl<d>O@);HQNQHrzPvQ6Mu4mK~%g
zYF=RO7#29}8F2EnaR8TmBb{nuZ-Hc%ZCqN>Yu>%Ry;T_$t&rBBOKYeZtzm1ATIAa%
zBv(`6R;`2si*s2wvzo3tR=mYHNCl}q)oy7&<M=Hp3maRC5H~h!#&z1!BQ8)t7$w!#
z(h1wd&JZtK5dNkoS!*FgaP@FASjUm!sAHUq<wUvO`@%*g@6XwT>CLu<(rKN8#@rw&
zX@3RwgYxx;PS_{u7-XEnPML;wb$IOjH?O?<`lojOqeXjA`o!Xu&pwc7HKKxZ&;MZZ
zn_7LS;ML#y*ROrlb>UL^?d8*(-%V0%jL{kpnI2j%*sJNJ+H=CPkakQZ-4D4y+%!m<
z^J4a?>`4enJ7u3ninXNBcvUL>>CF9A^hp}OxVpLqp;>bp+tJ$kg-2JLv};!>mtHYL
zY_!2dUkR;U$AbJ&l{?E-5SU|=-Ksx=fSN*%i0ixn);T`!OV=~^Gw9L%P5dKb(`h7a
zC|onWJ##<GK-(DlFp=RjRn=cd)pSUWncIx8jPNYDFA|ibiF{JD>XZM&__zk`D$Ch~
z@zC5;i9%S+v6_vO2Z&G+vbvvV^iRR}5KCt_VdE-6SlMJ7_kM7cF}Qz7)jFW*2nTp^
z=6(_Iq-v%UrGS`}b<p7$7jZ1DLO~m3a###4evKiaU%XH>$7|@T*o7XAO+<OLKdT0l
zRNV}nxWA8oGAt&_zUY1lB^b#c;gQZ46J1%W#29Al5W2wKKP9xU;U5Oz{u!SCAHv;N
ziHw5gmk9Zfrg`D#Z5)+waBM;!xoG2iw+ce_zuY3KNiA+d_3+c|{aOS>l?iSCdy8lz
zGjS8zran;i$Sowcf`ro9!8dU3-7oOClXSuh5D?RTN};N(CnCora4t&+O(Gj2msrMT
z&}EXad8w=|>$&LaWHrGl5=n078s4S~tkmO_{x*;RZX8lAomE~Q4pSM9d7V0kUYpyY
z*|ZO7E3}N~e(tbptdt#gqdX(-mub+fgAcaOgZt-zK(YTq9<RvbujKJnevo06pcy`J
z1k@y<lZjEBkW~xY5c^^xdRZb^y1c*VE)}LOoDz&H{bDT5mtb1%7gLLfXuJ7#VC!l(
z?>+>u?A~_>#C`W+fTP%8_wO-vGQw@(DH&b&+cLNRD39;R<Dca5&-~~<;p7<LdN><+
zlL@c)+~v(C++>XIVf<Zo4`Xn@{B1R1WnD^JLBix4J&*W^Oirhl5PTIYA7PZchyJAJ
zPxaihLh-R2#V_}X0_Q_=>nFtg5@UM9Cu966<hv^zueHoXsa*R1-JVBs)M=Plq9aTz
zOhd;U{7%o^cFe)&`bF_sG`ywEpTE3c*}{px7^hB6Z$EOPwrH;tF7&+G^N@}@84F8|
z{S~HZC8w!lQvSN<?mH&sm3~pQPl}~O-XmCFp(1VZFTzkUg1zH%3vxcx?}+}38%iv7
zm=!)$@B8+0-GcJ61#n-7QxfJ(4z;?ue;1GTpYr&gJiafF|K>+`X`^WIh;DAI=PuRU
z9vasSGsYjIn;U;brM=pex>PRgy}ReJ9+AE2#8NG%L22MwbSB;2)pNHB#km~C+xkS&
z>D`tX(;F}4qnEG;k9<?BUCm2{6HoL!jH6D#*pjFE?_mE%&z*L#e_fb%sLi+sh6RZT
zxzKUg3P&Xj+#@J;o-JWT9!1)kx5BSx%eXgEBrdY&DCyV|T2YBgH`CAd4A*m+MGZK`
zq)!wqyC25z+>g?~kI}!6<DZ4}l6hU7t{gyC#*~AL>G&gb+6sB}_h9RB+Y72lNsib~
z9qBjxnpU{;f-%`CMe1=K7D*Plf$w1xJDotTsTdi*>R#OEK!VId!B*sm)n%5uZ+_!t
zjq}=aO=1YU6jrwWQzC;7p)T?_N0<&pNEc@&a#1+5n@_D0t)C-4^HNsyu@4lV$x(>G
z?E^(Y#Xz4-afu2n961eisCpc>uIbyQc1bC@1JFTX>6h9DGXw~-10(VnlgETSrufm_
z%Fv*W=taNSbC*h}4)vm+7sejO)58~weKU3Dab(ep)MBe4ZwCsezuoh&kI3nCc8N}v
zuH-wDnNplr(4+MIt)BZ<D88Pf_*+KtV~kX0^2F^*g#39Mi`#%Q%pdkV%%ih7=dMuG
z!Q%hvx$h1Z|DaD4oq@~uWU>ykCH>||=1N?b?b>o|o_2y|TFwo(dXYEG#-#I0rD+k0
zIws~VJ@?)*F?aNf;w%~p4`fCPzjJdQ2o>Fyg`$eR<8ljfUb{5{GO>Y63EQ$|-y#}i
zfG}jUXPzEaS0|TnBtlcsAr4o1?zcl6F87P#mh*q;0&Q`&a9)ap=X*U9epH?hFO?Hz
zh2x2P?y-a0*ZM_q%eg&~Z(g@8rpo}~{BQI;h@*0Ta*1}8cncl(jCn)GE%^UyJ@?ze
z|Cjnjam)EXcD`$VvM3hb|8dU)I4bYQm)f(D1?OMxxz`TP|3SYfZaL?tHqBkDf}<U{
zEzl<Wtst3!@Af>9qt3weQUpp?G$kGK|DB$D?wEyt=odx%EcD^9FQRW@p)7IwKv7Wf
zdwqtNE>VGXD<2U!Y>oBCC&^lO-O4`AJ&A>=u;q@C*3j~ltW?j);|_VeSsoRBbeAj|
zTi4~Q`;%xTeVy*PFC|O&<|s}wiXY=5YGD%>{&5A>s#hKkgFPH^Yg5;56=b;Y?RmII
zWNo^*M4usGs#dC+D#fdU-4FKMe+RqY)h~*7<}-Gm%-9>flImk|YxF#rqt3@{c@;%V
z?T)#4rsuvp=HeInMRCjLqI20=Ha3T@YCqZYfQ~vJhp%c2?f7`ly?4yWv;CrIpOL~V
z-Q4^tD&CeWn3%*qP!v=w_B#-wBB>_nEOsO48y-0NE1L&6tH|e_){pVAvh^X}2VEcJ
z-0k`}yTbLMB%Ps#rK?XkR?S7YR4ciBI;57)sm%^t`r*w4DrAJ%qv*Py5T$dx;ea~}
zIP@%+V2LE!d%(F`Zu<gnLKJVb8&SN`wnYAxq|>zd0BrmbEj|!CulE{SO7Wd7I!@1P
zIdqsFtMTFRN&YBLwBM-W_LSQoUpcZVZ~8PW`wVQbL=HZ!;cuU>;!_v2;iBFjws293
zwp;iL34Y+%F%GZdsvuqL!7T%IQvf$heg&j&q_a-+q*bnSkd7OrBev<ZVdCz?BgLUx
zx*;H631I&2fXemT5`1PWzXU)d8da|}1-i<Z-jAfgs#3JeHz_fN)B24Lp%eZj9mJg~
zZt#~7KevhQ+*k0cl_Bm|QMBQHjsB<OJov}M$LSkkGy20lyolrz@w()Eh(q}s?$^2L
zYy6*?;{FYOAGqJZf28RDjvpAcI{8}~kUEK78cn_}MrCxo83^cn7ap{2h6g3^@t{Bm
zCxw%A0Qb?U^0&|p7%(cIMQUN~5MOL4Rhq^Z$_!jq<yn>H)Yk!bb-+Cxa7PE+&q0z;
z0euUoK;-_AJI$ekbRVJw))O~K7a~xePU23=c5#VU6FuUYRSTDXsLB|=nj`l&+=Wrx
z`@EQc-A!GSO6QHI)O~TtB(Anx-^cFcvb%`d=`5~Ce|SH?P;LQ|U&EkF@4gk{0(Lt5
z0sfR#jPu>@?P%woqJO99-x>US9-EL=To@YD-&(@w%bNQu`5TU1pFp+cwzlciW&S2r
z<#6ohO4vu#_a)qA6ds0ha+5#0P`N^vZMxBWR|#Vak?ka>i&yx1V5NmfjFR_LSAuXw
zUG0$*r0u1h=ikwEp-X_sBGVO;b_-&khl=9xBKA*n8Q_Umv;SP?Rxm>MPUaEbh*^qb
zcw3{ldo=8RdLv18AHXkw-%SO)9(s@qv>@Y%Ixg*zz(IpX)W>qtNp&KaZ@8s%7xASJ
zI#2nu?_9eew=QsmblLqJIv|@(n)pI`JWno_Z$_Z+&$d(>)z>Nj`Rx|SiSG9%p34&I
zWP?VqPXC_3zZYOT>z-_KyBATAPG7(`j&S{_PSi%SO`k5{lR9);)>GfypmV{n4dZ0E
V4COS^Nmxj_ibU6ci4oP+{{!6<Rhs|+

literal 21627
zcmcg!X^b7maTdAveUTI?$?=ocPFA*dSBJ0oBqfTpv*e1=QgHy8p3Hl1_RY-Bn|YjL
zmuo?R4M#LL89;(PP68w_5Foabe+dx8ITXW&?bwcy7)D^gKrSN*4CIe<If0SO`KqdW
zX5O*pz85k3<IPT2cXf4DbyanB_k3{V<E^WA@n5<awQR?~v1a+ZP8j%2%a5~k{_(`|
z>Q9!6K9)WBq3ro=B^@$bt!y)$tOvC?w5+-lX6eK0cF?ren~CLlzOx=hX7iF0TkEJ3
ztyc-vx*a#Y^)=Nf%F@v&tZ~~1epuTmNWz+h+O@#nb{bhaqo~#IqfZDRCvPIywZhP;
zTM?*DM<Odum|W{dZ26HB_)&H(OUGJa;950|bYg4k+~rjd)Z+hI(Ap23hK=$^AAR`I
zM;@wdIy;^jRW5(wWzVz1)yKc^yK(H)Y%8poepK1A&B)#}<I0w4oBJTsOkz6#Lmuj{
z-B@UOmKlMBp@-KV$<o=_YPLKxwj!ft#x_wrY2;;@na*1`YF<*e2pn6X3~G{iY{a(J
z1fqFilo7`DyoljZY+?jC-Z4W8fOOVsB~_yqMaH({fq&?AmYcK{&2W)hsx%`~GNNRA
z+qsdYQ?&rhs>RIgbn2<FZiQC;yaRSaOiyR&@LCv=l7&_jhe<6?0FEJ`EJ|nmqzOSA
z+d<egV^+AaNN|A%Tk>D!wWL6(hK7*k1*fsbMI*6U^-wZ?m7ZKQSqtjcYSjyBJ7|B&
ziDJiZ5F|-Y@IYD?I`SNUCo&u;6(sPFAN~-q@0wo1I<#V+v`?i&m>${YM>6}2eUJS(
z{z(^<3K=D(xeH?>tX%VM`?P(LYK}o8N%J!M0ynkqweJ%gBXLlN-l+0)f?tj8W}IzG
zg>ldH8;RMlbiouxVtST=sUwOk?@?w-gVVwlL$_m5`X*__sprBVh@W43PQ#vm4m^K8
zlZKN`GlC`=n4y?9j$gNKD9AW9<8u31u4}K_k4U3AC3(vSo55I2p(Ng3eamWuxhi!l
z_We?Kx^8Woi5DAT02!(Aoi^)rV>|I#S)h|4tdDI)VEip<HBS|qK|R5kX&5=+RdMJv
zp(a7>2eD;@);5&PuUSUaGGQ?eRHu<0>=`mEBV9P#+Ha7Vi=g`ZObd%?(Z<a8X!hsa
zgX|R5iWdt-ouDNOt{7;)%Ki}%_ne-nMiq95MaTGOb}Xx9?3tktPUXZbL`kcKi4YZ#
zYpSzT7&i+7D%NZUzJYo)!2oB3lbA(@)pER`q4~*0P|Q-%A~T8%FJ_yu?V0FXF?Y5F
z9-84kgxfS7=>G8*l##W2+J|WegV;A@o13J^^HNr_q|XBaz;x5}TTs%-NJ8koU>NtE
zxaHJ#_Ok=7G^^eXr{M>fx7VcYiS}X$vH{Igz)`UVT5wCsIKUv_KcjB7U>i4%aeww3
z>^Dlsb1)pXfeKZqv*~%d^#Ye$*TF<>UKFWQx&<bW=FMd6MFu9Wv%Rm2rl_a}?F!>a
zk8(1JsFwzLO^q!APvh$e)H3JvVyVn9S=(W0uAjFQyHAwi%C?gOTS+JMY~|^G+%;jS
z$JwRAsDMv!$lyNg4jWJ_5gyF2DX+q%@Z7ggiJZ7pTce9-$5jY0Oyy*=(n+o%F2sJ>
zewoS^i!!66^bAw=ofy-|J|*?1xW4j)u$Ej=2-0JLrdcqD3=yvb0z4;zU(Iw2<&AQW
z3~S2u=NLU4ydOK;4jQCmiNE6qdm5qiAHhk(>e*kHR^!|%aq3jU8ZM;QC|t-MEEhFU
z%hE-Py3opfqEa%(*9vG#DQC$5`^W4R=~39G{d8NURJaibHKoEsf>bD{V#F+Jj^<S(
z_!*4ndbxjC0|PS{Gfyk|38t%Qs&Zq`snZ;}OIpcj*d}78k`r}&_&%U5i2@pJi2c7M
z#q*345mha8*y!b46$soWY)mzY5&39-FL0Z^&>??I1{@A(5}}dv0aP|U>Ck?_URE}f
zeKG5uj!XowSOS!kPwbz-SozX>^Ej@85UK)umynG|tV52M>(6t2j6RHw_{gm!s%rBT
z6O0HpHo%-`)YDwDZSHamA%*sX_UjmGzutaG{&|i4TB$$B^<havvwgfL1vPxJk+kZF
z0O1}v9N=yw_KKjNRTHxxu7``I5j-Wh9r&gPl%x_Gyu>)g#*<{78XG2VDll@gMIe-=
zCsdTJ?aUfs$kHW>6%kp%NVh^GsB#3&k#~7iB}BJm*zdI8B^4x`EGrljp#;-H6s|Py
zK<W#C0xUzV1O%gs-B^(YKoK0K45K^6<1Nbbz;t*mMvy6$WZ*;!rj;LAW>~W+5GxTx
zb5^%iau$N9vkriuV}go!P|=g?-JbTR3LsiT(}#jzEiQ>mgCuSxaPN6!HNugVqF$y2
z!U6<42v-o+lB;3bMH$3Jk_XgL`SG=iYAhYdkc&`9jZh7Q`B66aj9a=@En$#Cvey^b
zw<xAla9S6e1hNX5$WX~4QHY@Vd>>1SLUfMMsfFbSIxe%nD<hI#*+(P9qs2t1eJ!JX
zgF$u%g-UA>j>NVL6Ub|)^lf$=x1zVMuh;7Snj6(E&)E&vd@Ek}Tg`P<_v~ZqR`kYo
z2x7I_^j2#`7%D4{aY#WJJ5A86?n>EF^2f*Dw*vq6z6Uc)$j=+sod}D%eRkT%-}fw4
zx~41Th@cJIh(eS!blXP}0`@9@th2mfVLf;wrihVLBfFK3sUr68^BPXe1~!ei+~%>n
z?jk=wtzikd$%DLnQJ2G|2L_u2?VRq(L51y!%@Cy&nuyQ2Ti3xl8g@6tx*025S|p#j
z@XV!4mCbXPpRBz7$;;>7bLs54^XH#_a%=0IS>E}{qO~l9unabvuuzxIZC-rl+(k6K
zbm^?;tOa4C)NGm-&o?l88sy#5@m3vyFG?iloD-<_5gbO@&my;gyalHM)~IS*YM{>r
z{U~Cx1a2<QOr9N+(xbQxE}54SBvYW$Y>`#Wd#?b<GRc2UESlg}yrk)?P+HMXRc^qZ
z>j?Xd)Q^LfXYE>^q1Mf`E|UQMgjDGC1Wb>@S&9vg`*3fh7)#QOLF8EwKqKB@(5!%v
zz2F5EY#0}xlH!s_((w<2rvxlvrhAk0uhfr30mV#Xm||C3gunnr0c2T&f|1ix^<jJv
z0@ijq)*JVdRT2Q!2EiVz6|xUbh|EIXc(zmr2_3x}Ia3se)^%hDV#Bsf*rUARLb(QF
zBKX;jV@yv85<5)`)?LY@1lSA09YVG-(%HoHYlvE4;u&zd=tTjFF{a1gf4|bX`-*BI
zbRWjG3ID2lzj!wM9Ebmmasv9Qq6U~S%!P@3E+FUD7FyB7zQ^1+rd4}}nigs!dT|dG
zHq9OQPf6KO!UF#Vp;p$V2zu#R;;MB(<DP^rh}B%c6m<OUfD#WJ$>~{Iq6{mJd)#lL
zN&4!ie5-=-T9s0mS_!r*d7f|PvJ=&io-}<hKguWOqVA@9BF<}2mv(DF&xw>1UhpIx
z*Lez2&XXE}kKtLd>3EnuiJDT>KGtlj*%arcW3PM1>d!v#`kzrIb%v|>)*g)*;Niqa
zT0qS062mB<%R_*C6-xawYPC3S3k_sZbORYgq#5EkU-iz_45w}&&B!4>y3>Yzk&=jT
z$h~0mH3MBCxZSb#q1JU4UOI+ETf;YLK>S~@4ce<gfY5S`9G1scmliaRkF*5rHf0Ks
z9>n@~M$(i9<~Y{h@K&)MV)7ZB|AH4~@@H$b;77&>Lojw9(~F|hHBPP=NTKLCuPUfT
z*4?#MOCrziR0|_s;0it2aDqTTgb{!uyh$3MG}ytq?f?N38C7Z~09F*rrEAz3q(z;U
zfh3x5QgYO&nzbEx&B)dxy1%uLM6+*@3rPIya5c0Rt{d@wOXtZ{2J9ph8`I44T5#Qd
zU8T{mSWhQ%2!{qs`KzvoC}7jQ_qap{Ckk-g+NCrNEv(WJ%U{KG%B!6&s;TaDx*<LG
zNKtLJs3t3>96_m{ohsyr)E}kk3mddb8S=dPe1QnnIsKHwN~l7sNm;^n_}xWYNwaA)
zdyu0zQ&ed>K4OosX?Tb#;1mkhlsFf``HH^VU&)b_Xq0SiRszlyJ*YM5Y+-KS4Y3tt
zy|<`JAv385rY7Y<Fk1_9N+QUsN!ssPf$LO(i^q<If<()6>q!)@R~>)dc9PifiY6s?
z<#?sdLf%FLidL1PBgDVFdW2=bmIaonF{VBuiGoqkEYZ{=aYY$eE@UNLAb-(bC7sS)
z6<h@^M=-m1iNp1JEaD0vc}TrL(h>J{#27SL3KGO2%_{(Bp*hE_T1+c|gfr=gk0to7
zUTT$LovVi=sird$*YhR}=F!G67zU2?Rf(8Uj4B;POoyB`w%&@(t68;9&%NB(6}7LG
z?}zDqHhY57_USlyBzg1~u~eD7o*+XD%Ssk?B#98*!Lm9&O5iDZeUOgFl-O|)%<64{
zbT&eQ+1SN8%?c@f_7Vn?Z*ox5Qf)qAyN~k9(ONCrIG&zX#O8%I_BN2~k7?9*cLE)i
zx&ch@Q05J>0l6`pCn<C>>oMUv(}Bx1cTLG%5gAJzP+GxJ`N@uQv9Q_3P*?x7d4&d@
zWJPhEibn-cw(%BhF)8CmIWUM-@-x{%y4Y5Zl^XKl2hen37h>3S9DJeF8HJYMr-fuT
zJUVSxAV~_A9i%5~USRGR7C7t~@b|Qb0PlP&oo->9fz+4HU0Tu0-@U!PH5n8wmew(?
z)=@KB$1WeW$ahdk#iqmUS_uc%>9U088N23K@iyb2*+}iFc3b;d$8XDC*w|f!=COq{
zZqVi)ae-pPD5<uWPTD3miFgHrNH{&k6BtSauMdxdB^}w2I>xzF&YA0NFzi|KR-HYR
z-fo8|ozdxN$OidI`ztUdl)5)`?mkJ!F%KvL6)|+`{l#<Ny7G<hzOeJp9dm}tzjg6X
z-u!2J#-QLQm#%y={X*M}lhRMUA<<J$3V!o@f8#pvy8QOl*ZixSq}V&7Wg?P6w4|`t
z(kZnqg_R?1s>+T4^aY{S5Y4EMWiMn;LvcDOez9|UznHndjK0Vi+`qQA4kcQ5nhpH;
z*iXa4=m~_(6jVfOE!y5&D%aUK|D=>w%B5G#5c_nn@K-`>*Rh~;X!w%5&AqrTKfqYW
z=MC(7=Kczb+)v<#NKR*v-J!V7^!CjCC<DRcz-A&9YO1QgimK_b8acNaWes8(xfwx8
z*T{KAYd$$jST3$X+s|@{VInm5R7Me|b-ZTdhyp@c#J28d82wc^DPrv07EE0w2rFA`
z>fQyuG6wf$s@4TfM>!IVGxrYwPpW1*S&E!#Di1jv3?tyB<tk`{#*T<Z#((3;{1-12
z_VHr-8n&y)ViVyYZRD!KBvtq0=*0bf{K&AFDEor@M<~HaK8Hs-{hqQlZ==2)<o+=s
z`zC%sw)<r~|1adae@>kjl>Q<i|KXG_zSqV{3J0eu^ofiPZuhDnRR6;rqWYI^PxV6K
zLM!W)7;4n6B0b<j^MAL~?EVYhA++zw<KN}+eR=!`KN4oD`(Jp0>}lHGhNC0Tut#qb
zx+)VIriR+2-8T(nrfx&S_*ES~w2@I13ngdTDH(X02#bD?S(K!cUVvDgwt5QVz%x^3
z4k^3Knn?=evb0Go!dqev8)BD<!w#$R18if&PE1u39CeWld~RJjrXd@Y3ChtM$Wk{C
zsg};E_yew78Lb7K--k^x8=={<4{0m3OynN;uxe}&x@=ZiF7B6T_-qLtZ<mPsRY0Jh
zUz5k5%H!+u_y#}7s7quI?>q`>lF-S-AWzEDitU$uK@>SH5iDK4qwg*irXHLUjBg$k
zV@Y0u>Cr(kwW)}<*^dBQPn-RwLjWu8+Yf=b=MDqh#{Rp138~58t^-BM>brj}V*R!}
z{#G7;FOTo=qqnTdAHm~sw(>Tz_WSPgcCy}KjP7BqU2zZN?Vzk(+``cvY$jXv%Hv_M
zhX^%lxBa~;2*W?x_vnwv@N{XJ4iqs}t5r>v@*E#RuhRdEefO_W+{#g;1ERo*mfREy
zF$aw46&KHJ9!IQ32;$mB(+LzxKGXM@jw+V9<vdFv)O3mDclz$TOC-NND2m@g!#gUA
z`I0OoXHfP!X*XD?`HQ{>bX0jPl;t55bxGt~efQoak#7!)qEjN4j>wN-n}v$B&G867
z#YFax%Pq*U2OZH5xS@nwhuP>uZNR|puh*KPta|Q0!DR_^P7b#_!P^Jqy_Jmu$|E|#
z#lE{#vOP55nPZIqk4|vn36-hq@O`CnVegyz9_ta=n@%p*avIbOd@VYYZXfHrTZQ7G
z9L2)}qUiQ?tBmQD*YdGTI6;6ES-X$RONA59_C1WF3SfNMQ~h_b|EK%zw2S@E2-6O=
z8E=JQL3Tv0qa3#MQTdD`tZ<7I4o~DUB;9!<|5~<!TQ9|GKf6hJQl#99Tsf5#>2i8g
zId%HCGZl9;v#2>|!Sv~f75C>bSobFV+@hbKr=Ju*7Sdqm4Ru`fII>5koWx8go}lAn
z*cf;#_EH;OP(@;O)OPAf7UI7d)j?h`E?d7ypl-lO$<jFRJ?zS-lgNn`gXLG<i~CWK
zAc844jZC+?o%7J`ukawDh#LiR?_(I-E>^bj<D!-kp)N8`N05*rq=$bKRVn=2?M=AS
zwyVTvUiQiq9RS5Aa};8O2S8C!F+CttT%rPtOipDSI%5u72o3CIdnCEqoa`{BsId3T
zeGja+5uyS1bh2(?`oGwBUtPB6^TN)<IQh!2Dcf_hWhQoHa)q7W>3fJrWM?|F+-BMo
zXA0*2UEe)-G56bpqA2FcUx|DUQ|Lig_7hiexU0f@4s9YRl?(qTNBT8hN9F(IGTql%
zWg5DeKh}4*UCbXI6vZ89{=((`$~LaI#kgW=di#;n5n1+ti!j#u9@0^TvAEpaUuBwB
zbDFw@^7_8J?-I(&peQ<pGJx|b{FfNL0Z<fFe0I>Ot^5~nZX9NHU-|gC$3}^}nER|o
z-%{zVS2U>G`K)^1eRV03$tVU`0uJo{XP?6Ebg^yMz6$9C%3QtK_c)Kp({yf`E_AHs
z>9(wEqJFsVzPot*!9jUEs7LC|SGKvOPN1;((|r%~=q%2;+m_5MqJv-WyYDU*|JtA^
z3M=#pk<u$29du_a+oaJA7I}QF?*ScE9)~A03yFNC@7}v4@})shbV_6Z*HU;VnR)}D
zD5!Y;&gjMDChq?=<k(!BMw9`f3;)?SE03xRQ_DDgsHx~Oec$i9-!3iqw?R?dasCgV
zr$a(*oR=cu`Kw1?nOMEcji)2ay~FhT`tGrd+h+zvamTqmnIH7(h|kLa;rtVQ58~+B
zPG=+dxEVg_A%{N-n|HSFe!KYpjzLk}asH2=>$y5AiiP)$z6Wqr-cKwaz80$Y-D?-;
z%|TJzan4U~nY&g6M<sDFuS56SK_Y=)=zAbXmB7q$1WHylC0+V|tM8t>r0~L^C_1Gu
zfWt0)zAR}5Kv7Wf{z2UqQGtvqA9d?{MLKA>UmTAsyEC_vuSvhyA(saL!Rf5m$m2)l
zu_BMx@uRm=(Xe{2NzbB{DDda|?n|lB+j1129TdeIa}<9#D2j)HBB>_n9JYw)voJV9
zE;~9n-^!=cHjeRez>Q(voZcAX>^a`Z(Qiz!<Ts8b=`6J`U8=(=eJ;XvZP`?zGluEB
z+K9q+GTz#uLdJ{zqr-Q1qI913fN&)S2kGUGHIYZ#K{%Vu2wviSq2i4;h>ADbDJtG*
z%P4<K(iz$q0&f0d8y~7((EC7brTC~DUD)7g2HmH}YJB}*ioXCA?Ki8qs^|KoGNW7a
zrcYF}reHrTa_}7&zj3aL@2b%Ln0kNQ!mT{o599kv_y-5raR3_kQt1{MuC%CYDY(Y;
z36Q>-&N<Q3R=LhWI$@NKX{R%WiHkN*6bHBI4vKt|f?4j7@a{_RO}G4-35{q>y^>UP
zm2tg&OoLUWXqWFPL#i|SjjlNm{v;j31wL-@KTu5fI=XXzfdASV;tq{rH106{rV~8)
zr^2V`gLJd{D^VOq@tq4@axTQRk4<-!n~w1>GsPXp{|D{_elgXj_<>QY)8nN9sn2(n
zMw9PiQW+hQ2Ld{*hX?I);z1iKc#zKHL1qDm&Xe>wzJWk(X3!h>FeabkYUA)Q-=HZ~
zn!#7`3|x?A;YxGr@_>6h;0_PCzXR^>fO|Vga(U2Ks0wuMqug~49ir<uC9sy_5Z%8)
zc{+vLP>tgHxF&tnGpiP^n^Bc<e6LBa3%M789ajMKcLmi2y>!92s=ibJ1;wSR8~fN<
zUUA=z+UXoF=6_&6|CE6RNPg>wKDXdoA>WpI4}U~0#)Sd*656?!>1UIEp2E*Zuz_5~
zRkd;bl`niaueHCLzu_GJPoUaLN85DzGJg%Naya()mavbiFPpg6P<R;1sV)B8N979L
z|LR5W`%4(xi0mXeUAn>-Q!8ymVwAl5y&8n8>dKfL3+^oKzEFXti#-lBvMTk2q`eMZ
zegyLs$5OG;o$CM#UP=FE=01ZFx<AD{!W%J5aSU&Ddb2dlrZ>`O*TH`PdsIM^$!&6h
zR%G0Mz;#hlILxC_^_ix0N*(j&yOrtu1$<+MPRc&xJJ-+4WgeUhUU7c|_{f0Me0(WA
zk*~GNmuk@Wr`xKH=^HtKe5ws{viE(Sn^{7ge3(Y?LHfCgpO;`r>z*7*aGyg#I&&Uh
x*TQYHI#C<R5sP#YmjdaYwx_=KLWjL!AtuO*8OnpCQ!tlw^NlW^6C<i?{|k6)zt#W%

diff --git a/docs/build/html/.doctrees/index.doctree b/docs/build/html/.doctrees/index.doctree
index 6600a1f181a93a3a2877e62b845b5f329ce9f5cd..e2047f1917eea310a066f60e7e0989f357f5d205 100644
GIT binary patch
delta 1037
zcmd5*ziSjh6wY$DUQ8zzq8|9bCWROO1qDGb;338$jlyL2?ao|gXD0K*y+dTRuuJ8x
ztzc&>3uy!`wKtH?Mtdt;@$E*-bfPwod2hb?=Dqp8dAs@PPW&W(aclie{BAHjh*nmf
z$Jgr7@LL5_4+@1xjutHL1!2*FGnfb_g~JpQU6|mR7g{k1xG-qFTT|KsXErUFMev%|
zDwPNn!C0N3bC5F6`hw@dLBbU5AlRTlD_~IQ6rCS|WX5aLejk2};_a){S^fUh>wn$W
zxnFH<G|!r+&EsaB|3AI`ezN+)>a6;Fk0WetUB3;PWd)Yn?gEoimku&gC_yQ~VP2p*
zR&bJ8L=Y+EA`?lkD(I{SPW;l4_B%@u%42S6Q{|+lAfjERONnWY1YYY|JMg6HjY33_
zqe5^ZSImdbL8b8g*a4Z<1?l~eS%H4pUFHl?lb3{|6Fz{qOu57gGD0B|2Obly#9lzR
z(eTmzhM(C#Vb1Dr4SK?y(?2$7`*QW}+4{%D8}-d`6+LJ_jK_oMRr~eQ!C?A`e#Lx2
vfgkb1x$81RA?%-4q<ODe=h1nGoAIMr519pizAN_UuJA*?n49*?<?ZMv*Iaxc

delta 228
zcmcZ{u-l8Zfpw~Z>PFUm%#8Y*k1!iCZmwlL&dAiWVzM903Z5ygQyQn#PSMC<g$PXE
z#_4M&7UJ*XuTY+mSfY@UpIWRC9PH=|WKGFnkDZbs*n>lQ^GWU?VNQ;c(vtk5%*33@
zV)C9$Sy7W?<eL~1Hs6<*VP;&s`H#{zX3tti28OIEAdzuB<4RU3h*tz8N_#l-5_3~a
oDhpDJK~Bm7sq@RY?gv)lSDGOS5(Mkh$+(hHkyW($w^{@v09$%Zo&W#<

diff --git a/docs/build/html/.doctrees/installation.doctree b/docs/build/html/.doctrees/installation.doctree
index 7a0aadabccc94c7e11f8daf3966d0bde0113e17c..c3f1542b02e980baea7bc3bcf97801fa509cf2e3 100644
GIT binary patch
delta 523
zcmeAUKO4f@z&h1QYa{D?c1DxQ581VZQ*%@EN{SUyOOmH#u*Xix5bFVpGp26l=Fn$j
zl%H(Px1CXO@@KvujB1nL@K0pa*jy)2%*3cQ`IFFdM%~GE0uq})39n*eGy*fXialXu
zG@Cq2;wYoV<OInNj1HRvr2-fkohL7n-pJ?*QZw0H)}He{BLhQ*bk<wO$p_?21iXMu
zevpVv26Jgr#?{FWWv{YjumMGXPgan$XY>K-(=-pMEJ#(z%u^`INL5HoNhwM#E>=iN
zEK<l%Q>e@@EmBA-$}cZYEwY-tR$knjXw?daM&^13Kxk-XYG7b6rFBZ<l-em88LU~n
zOkhWHPu?$Q$`}InpNqmqMh<C+xFlFSY_hRZGNan&=}K8lj8U7JRQEC0n*bGL8G=;J
z$SBH~o-rkh2k5&jP7t93lG6kdr9GT^iMgpIKu;BeEX)Gw^2?afkulv5tlkf-)~_@}
z5hM#Xjt6L5amJL4Vz5~m^T7szgRZoPH!VNEBrm@tHGZ<a<}=2O$!c1g7!OQl)Rvz-
UL5z)AI%_YG?a#P-a-g;q01DlqH2?qr

delta 689
zcmX>b(jCs)z&f=-dn4<7c1GjLOWC!Aa#Qn4iWO2zlBZ;_$4<!*>j4XI=H<|5W0ae0
z%eS3TVe(hLAB?J#-|<gmRNvenP|U=rIeCtR#AF`f^Nc!^8w4aae-U2A#ApC!ZWnvP
z$Y=tTKgwt}IZ5&Zhi!&*)(%DnhRFsT@|!EAv=|xf!MgWI&kT12%JBo`GGsECOOrA<
zd-zjQ(=ziiOEUBG;&U>KOQuYoqS-j5c8W#@YX%$Gft)=eXlmj!OHy-@6!sKP&X*Bo
z<eHo*8zaO8_Lc_FXqJ-HB9OAlsWKiMe?XQ>XZ@OdP*hXBG($V<2S`9RLnlMd+Y>19
z1;_<EhznuaWIavk$xO0mIkWhgz`A)S?^iJ8a04pm0t$fq$CJeYkpk(T?9V1IlJyDI
z;P)U2ph~8!x09=-lp^K)3sUnGl8W-ni&Kjf5=#^ejm-57fY8v&)WE<17Ab_3wN8PC
zQkFi%0lFZ!F?xfegiU@UBZn<S+!`$IJNc_ZGNbC|NX0BB#+uDXl=m@bhXEC21%p)0
z$SBH~o-rkh2k6!;P7vV-lJf=<r9GT^iMgpIl?AEAplHbg>GI2%(UCFT53Jq~tk$nI
zLlGnkHjW2qTye&fjAF1^8S}HeC%;wy#n?6Zg~le9M?n3+@K9ot&bkj_%1nNwX~1}Q
IvapsF0N7U3*Z=?k

diff --git a/docs/build/html/.doctrees/usage.doctree b/docs/build/html/.doctrees/usage.doctree
index ae5fe158718c1353d5bc12769927ba9e69c4bfb9..f91e526eaecee72e6ed7f0c37ee9e4583385816d 100644
GIT binary patch
delta 5207
zcmc&&Yj6|S6=r3xB#W1M6fm~MwGBoF$vkbK0S6i5*cclJW5=XCypmShmDiHdt_<$r
z+79K_I8EE5OhZFTOEbwNnNAYacV{T+H2qOXfK2+Bq0^bt7D!q;<R8!p^xS)`UGW&g
zjG5LmUfp}{`Ofp+bI<P4tHLYS1#w7xp<wSj;&V>n6Bx={F9cxNRb<op;h3vw`2sZ-
zlJ`_9Mvu0DNU;!64YFI+G@=_)!XRpl^v9D45|YDGQo|)VKmriY>&TX}5f-~zvk9j|
ziyl^1BEDOf6P2m`so~T>%A<%Q4-HM98oyc)7Qtr|nu?iSTo&=f;s$A4U*V$e82!C6
zJU6N33+RdwCx#*uDHKY`x=sR80xnEaoQh+6N}16)CPC>7liYS8l)gFLCkP?9IlTz#
zX5{lxde@Au93hhSyK@Bi{p^a#5jiG%3I6TH|2<xqSoqi!N+W)xQrhCmDlcp;Ty-aP
zN#znRbo+|oRACWcsWthRd(&47O9ZARSAc159~+*wO&6KA6nAoj&%j;s(j?m+Z-$D)
z^m`@4!Ys$A8JUI59JZCcG&Pr+m04kvv}5l62Y`;xLlCvv1kp*lx!eTRnoC?$trxD$
zXPTCqE2s&*1J8hMa!|&NNi&Mc>n9PIv#=^Zi$?Puf$uM_fuThQ^Sk9lOxAGc#&p%_
zCo-(^Hk7ll(;#QXn+<6wGvswJ*|)mH6im}Xv%=EC6XatVdb+R(h;JdWI8h4Y#Py|o
zIGVJEET(m)xMf-SgR6zbaLspXj84v6T>Y>T-n%D6>AoeG1!!I2B7zxy9GPb``fSd)
zaY|wIa1Kc2%f&hz9ssF&0Sqmh>&@(yOtQ_n1wYQ=-?QK^-vz&SLu6_HIfwt$g8yg~
zKCgl$aa~5YeROK6KF6^iSlH8}SUVi4+Fm`uN}}KN{Z67K>>3yLZ!WAJ!|+ckOt=EW
z%gV~{JttW{IC5D8#atReJB8YE;jf+wj`fIaXJy<Nomq<A99?9g3$oDQSXr1?#aWhF
zEQ=Y7?Me>pnqL7Yt5#+^YXv;ZStMFI+qu9tF0cVDZsh`-k>V+3CNDKZMoq?<1=lz{
zYQZDf@bY^LL>71-2M=4|uVjJC;N$YydEenYFIqe=m^}A!c%5l#mcvN2EdB)-_%kkW
z13LU;F7O0WJf$?h%S<7BVu8<d@L3Cd=5Fv^r7cVI6%M{+f&Z2To(H$q%*wmXc|Nmv
zZkjyYT{|S_yVK`uW(vMen=o$N7QFLfQjbjHVRrw~v!RoiEQbiaDFZSI#uEuS2$R>s
zl%9A(CVH<NRKsde(y&W-W9=OHaBcY`lXcPWeq^#fTsv#375h4oovm8f)m&xYgn6qG
z@o1IWR*Uef$7jOV)}42Da+VIt0x#C3oVz$7jszc^o1VK?ql6+QM=4gkio2;J8BiXt
z80}3u35K&io*)uoaSF+Xq-q#Pc~7q<#Uw+G$Kc)iYWQgVN2LAp8T}8#v?3Qh8Gw!_
z-V_d@l@)Ni+W|`(+MNfu=>zHK8;S+nfC!TdmW!Rptik2Rg~B$NwqbC^-M64_s6EV1
z;%TZ|U%`7l+ycFccvKD==t~^?Bo};hBZ2of{K5GaSMo#D?1hu96T~1Ycpc8R&J|9<
z#Et406nMrgp#*j|yWr0)Ys4LB)i2X;HZKvJA8?D$&=lJPlrCc7D}}EwaM)hwLv7Re
z0_w-B$eIj92QaId6p!41Z)_?aY-{s3`!v;%Nm9qdB9SMgq^_${jEn}9^_F<BMyCOs
z?^Z*GLOW%Zo-f*ImL{ZFL@vdH=fdt&jwE>G@f?OELn6I#r0T@ev$@5OXD)8&6(o$i
z%TPp_V0Pflh7ur~tHIM6aQ=(C^@*7X6&<)l6EV2||7-0adWzOoW^S#+kH(yfLq}Qo
zE)Ko?-~blfFM>RP?VB6LFvjURq@H}=Io{6dLmqs(waQMzciq|<m&~0Z(v??1XqzE+
z7URx<g0?RYx?FypD6-Z|@Fk*G4R+)E4T<;C!=#ZuNlVJ~J&6R78dPLlrs>C^5Sbr1
z8EsTUAq@|jhBX&ot0+USl)$=d$O$}ta-S;iu5h7v+&}o<g3ENz@aDC|P$YxsN<68B
z2)-}%;aiMOf=MGD4)bjU7ut3>E4YL6!M|mteHXe>W`}dFWkMHhY46I*<cH0sWnDX8
z<gk@AE`u7vs*sRf_ePHW&%7VJpZlNdy}9?sZ0O*a^7IgfTGv$r4|_fRVHZw|;%<Rk
zTfMd_yIHX?gS2>I#hO49N-Gv+hIeWRob7PfG!fp76r?}xxNdVQTws{yQPh!JOD}wS
zfiQJH()FaWFlulHhM5h+UwX^=ET<f1M`AC9h#<tK!GUf2oUib;<1l6WlKf+IVqJ?v
z>CM~UusKg~mbWQ9{~3g5*s!XufyS<-_*GzU*B{yQHTaL@VWZ<&clK|%gkLiQ4xxmT
zc6w*eUd_v0MjpS7TTpBgHU)1KA3)eZDtZWiqW{20wtL6mRHQIH6naf?e$1s`X7)XQ
zr+vw^5nd$RAt~2!A4vuK8pG^xOV}CFhDpaNu7_1Q1bY<?b|{Vqa`fdnQ7WpoJ6OyA
zZDs`va)bJqFa%xG-Eds><&|)@Ih4&yTao-CO0i;o6lO(#D+FP<rxr@OTirf$nQj~m
z%|VQrd5?iVS^{r(&$CrifgbD{oc0<-M32BktvJ&>_+Y8FpUL#Y4ecNs)!BRw)=PXB
zO)dIX>?z@Bx-+)bCVVx0qW32`_MKG9Hi#Kzt5nn&4b#U_nu#OyQ9zex(8p8su>~K=
zkv!UfvNw17l_$CrerL=MP;?7JwlGu+L$oB763Vj;fy#ua152>tQ~sp<K)J2_CAu1?
z(TViI)Yj4wQ%n0cu9of@rZ!rXu1}5^rYd<Olk|Swkb8Fa;D;Y6BEvOOG$^;nuy5l{
zPj4J=_W+h>LpAUj?~@Z6UgLz`#&`?i7X)nWDqUL=GA2J3p<l_c0LK#{H6|tci6QTy
zjdT#31T5Ree4XfVTCNj@S(zetYf~PXx{E_cvK5*YMzLc8FVpl_<`zc(?!bfPt{D+E
zxlh(oO~ObnO-O1ax3Q&u6aG+#Q%&nf>^gq&3(6_QOKZkOng)E&$5-BDK!PXxn*IwC
CxU^RQ

delta 3681
zcmbVPdu&tJ9nP_Hotp>EV>HZh9w%`aCUKkxfx%dC;=Bk+ou&{%w&M1N+;Z*NzQ&K#
zVaXtBDI27s>(6W1(yD8PN*|lr?n>SM*_LkW)Tv{WCUs+|tzgxpHUlB1Nh^~mI}cy`
zCgV{SDJSRr&i8%4$9de7Q=g(|E+OHt@V)O&y&*g<qL1KcelPOCnfyxAbP)cLKiJgZ
z4^PTTml6*J8*p63YD5lWe;oV6cv?+F@ud8alnBQ0m^^_!FqOaCNPosS7=nKm9NO);
ztw>aTI3`D3sUxYm)NIP32=lk+Xzvw%6(JkkbJt)si-e0{M_7&Hf!_56Qg{-};kX=y
zgR8vo!7BAmz>0Rb_)P)zXkWg&385a4%bjHKWciF4^=riyPE_14hh<EEX2@?6!w%cl
zGG^;a+ge;3F@}+*O1NgLEL}F$>T1Ps-nNBXJsCnf2JEUL_zI9JmzXCrg5hdcx~t9A
zyo1Vesa8tK+nZ9#=h*=E)-DvGq;5k=%~Cgq$}QZfZcY#3Ir{?qVVg}Gt3P;C%qMFX
zO3WloolE=LQ(row6Fm9^7xlmf2O+e$+I2haYv&!ars8fn7{u}Eh#bQc)3_gkjT=i0
zHo8px@J8d?@XHA+oN&5pNjd1x3^vq^b!nlf87@1!YN-TO#d^IlD>z$@CfX&X@5dRG
zUSv$>+W4ZSSD^}?bv9;!-OLART3j2_U6Kmcu*-(-ESFGA)8{2@183_|S^(|$tsf$Y
z;4i`t-MP@x-q>*CMa&+RK+2qxqu2sZn&CigyU;_rCt$JNn<lPYC<F0TPJB5_e9=Jc
z)>o1T&}|_8iW3*J#Geyl3q0nohH3XIIJBv)tsqnRE?vlI%AEAT-?-R$CT8g);eTL;
zImdd_IWrWmv%?>^Rpejgn15$6|H@#lci8Lcdh1?t*&wT5lFQ0-7hKu4k;xb48s*>J
zTp_OGkhK{|9fP2AFz2@G8MS7^&(zdt%6jbQa=lD$J4wjH<=imRQBPxSGsfCxD6Ee&
z@6RyDvrM~v<#{v^6Py^!5F-X6oY`s<=Q-k7262=jOk|gJjn>^D$;|p^lQiyuA91}`
zh~5^{Y3}V5Nsxp|4vwB6>t`$TYfgHLk$$m)wCw6I<aUme&N9+_1`@r*#4CLEGMl}~
zb2`Ox(x%-WWSYMYi=E}gv8aschaoBl<tZr)pLKyK#c@!UVsUuAyCyqW^i&tR*X!S*
zJ7?GYKQ66h*&=Nc*oJL~w}zasSd(uVCR?aQAe*)hxnQj46LAMeY}XMm+nW;iaic_y
z7NwYQd@$HoS!qQ%IelsrOXRyPM{t6C+oQ2Kxpn>F{o1j<0%Y~xY#NUBZGxr#!doMR
z6!E3Pz1v?!2Z{6buy){nG0CG*weJj6p<I=W;6h=Wu!n_pVMinCgjIuwY=b?$_+dZ!
zK1|3s5>*58zPLPz)i8N=z`Pg3M}vPBpXXA~5$(;w1QA$(&xY#JDY$r#|26`(V)`rj
zdBBb0Pq?So^|}f^;_b)URc|YTpL#n4i4LK2)D9=^%|i>M=d#j(P7+>XA}~uTo!L0w
zhtm5hO$EE4c4T$QuHl|x`fT!t{c*n<cEjP3pNSuGZ|}3b_7j=2G%wRyMyXgy(N7eg
zw*Sv`cK=-Fx|cFp$V7VyEW6IYZ+3PF)YDQXiL*3`Dr%!iD3ywNWg>6G;%+OP9+gV*
z0C@w(@RUE6kb?f0JPF6gt=05#r^vwwCfQA5DO{jN;{K2n#8Xl*A;U|%eWK06cC;0)
zj631dP?04>{M~JV>qBdx#8HS|hRE21H<oAbz?;jv^s?MSqV3iZ8eW|NCl9oN1iH}@
zAVIFP&|^oJ+eG5+8f_|~q3flB)&>kubmp0S0zA-T)&BIgPfg+w*VsWcwjiHY<ZD1>
zeqxIyl*YgwKFRPEF!8`^qRK5H>QYD&aUbk_@M-be-250ZH?5|J`4MU$%cE2&PNjNq
zM%y60ViKR?uoPvNe9HhMtJn+;lWpWRzIXC3tUV3y%MR9i!EoEW#1&qo3YJHS!V4_r
z3K!o+%iVg3>^QXSzgiU_wAoZ3Nd5$VM;c>xkHGWauxXNV8i{AP`nxQ?<ICe4*G2=)
zXqnQ-H&R+NH}DYs#{*00JA5CxAIQTVq+qZ*eZFrFnG!GZ7?x-Z0?-)18X873aG<Cf
zj)t1@g*>)B&3SNPbxTPO9c2rB60U`Qi@M?2NEZm|NLguS+N)I4dQ5|&-e;<yWXFd2
z+^`gqQ-L~y3LGaTod1Fnk4Iu(X>N`L)p&5)wNDK-r|4El-;kxSCUS)7zr(%ckqD_1
zc3=L0407P_2gcAzts^>aLW=fu{7ti^o9cJM&ZK?I*NK<F9@-oxi3VnAbB#9tq0Lqb
z+)SFpd_E10y~FAMSb=VMEm=`R*<Qx<GM1Myya}b2VmjgDWKBI2_mInti~FcACQdg8
R6A$EQjnjn){`$?q{{q8uttJ2f

diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt
index 06b4c04..a7d27a3 100644
--- a/docs/build/html/_sources/index.rst.txt
+++ b/docs/build/html/_sources/index.rst.txt
@@ -8,11 +8,11 @@ What is SSAM-lite?
 
 SSAM-lite is a lightweight, browser-based implementation of the `SSAM framework <https://www.nature.com/articles/s41467-021-23807-4>`__.
 It provides the functionality of SSAMs most popular and widely used features in a graphical user interface
-with a few functions added for convenience and ease of use.
-
-
-TODO what does SSAM do
+with a few functions added for convenience and ease of use. It neiteher requires specialised computational experts 
+nor hardware to handle and process data and thus can be run on a modest laptop.
 
+The SSAM framework allows for cell segmentation-free identification of cell-types by integrating prior knowledge of 
+cell type-specific gene signatures with data from a variety of spatial in situ transcriptomics techniques.
 
 Citations
 =================
@@ -60,6 +60,5 @@ SOFTWARE.
 
    quickstart
    installation
-   tutorial
    usage
    solo_vs_server
diff --git a/docs/build/html/_sources/installation.rst.txt b/docs/build/html/_sources/installation.rst.txt
index c1c0179..f60d27a 100644
--- a/docs/build/html/_sources/installation.rst.txt
+++ b/docs/build/html/_sources/installation.rst.txt
@@ -14,7 +14,7 @@ Supported Browsers
 ==================
 
 TODO
-We should add some stuff about requirments etc
+We should add some stuff about requirements etc
 
 
 SSAM-lite-solo
@@ -27,6 +27,7 @@ The installation of SSAM-lite-solo could not be easier. You either clone the
 
    git clone https://github.com/sebastiantiesmeyer/ssamLite
 
+
 or download it as zip-file from GitHub and then extract it.
 
 That is literally all, you are ready to go.
@@ -45,6 +46,7 @@ To install SSAM-lite-server you first need to clone the
 
     git clone https://github.com/sebastiantiesmeyer/ssamLiteDev
 
+
 How to handle signatures ????
 Download singatures: https://www.dropbox.com/s/8qxkgg16zelg6ya/new_sheet.tar.xz?dl=0
 Place signatures in data/genetics/ ???
@@ -56,23 +58,30 @@ Next we create a ``conda`` environment (TODO we should provide a yaml?) and acti
     conda create -n flask
     conda activate flask
 
+
 .. note::
 
     You can set the environment name to your preferences.
 
+
 Now we need to install some dependencies. TODO should we provide versions of the packages?
 
 .. code-block:: bash
 
     conda install flask numpy pandas
 
+
 And start the server.
+
+.. code-block:: bash
+
     cd /ssamLiteDev/scripts/flask
     export FLASK_APP=run.py
     export FLASK_ENV=development
     flask run
 
-Open browser at 127.0.0.1:5000
+
+Type in the address bar of your browser: 127.0.0.1:5000
 
 This definitely needs to be explained.
 However, somebody with a little bit expertise should do this,
diff --git a/docs/build/html/_sources/usage.rst.txt b/docs/build/html/_sources/usage.rst.txt
index d9e2918..e565068 100644
--- a/docs/build/html/_sources/usage.rst.txt
+++ b/docs/build/html/_sources/usage.rst.txt
@@ -12,15 +12,15 @@ read :ref:`supported-browsers`. Connecting to SSAM-lite depends on whether you w
 SSAM-lite-solo
 --------------
 
-SSAM-lite-solo runs locally on your computer. It is executed by your Browser
-and to open it you onyl need to navigate to the unzipped SSAM-lite directory
-and double-click the *index.html* to open it in your default Web Browser.
+SSAM-lite-solo runs locally on your computer. It is executed by your browser
+and to open it you only need to navigate to the unzipped SSAM-lite directory
+and double-click the *index.html* and it will start in your default web browser.
 
 SSAM-lite-server
 ----------------
 
-To connect to SSAM-lite-server, you will need to to open your favourite Web Browser (not IE)
-and enter the correct IP address and port in the form {ip}:{port} (e.g. 127.0.0.1:5000).
+To connect to SSAM-lite-server, you will need to to open your favourite web browser (not IE)
+and type the correct IP address and port in the form {ip}:{port} (e.g. 127.0.0.1:5000) into the address bar.
 However, the IP and port depends on your local setup. Talk to your responsible SSAM-lite coordinator.
 
 Navigation
@@ -36,76 +36,80 @@ by uploading your data.
 Data
 ===========
 
-The Data will be uploaded in the **Data Center** section of the tool. By clicking the "Coordinates" 
+The data will be uploaded in the **Data Center** section of the tool. By clicking the "Coordinates" 
 or "Signatures" button and selecting the correct files.
 To be able to use SSAM-lite you need to prepare your data in csv format.
 Two input files are required and must be structured as follows:
 
 mRNA Coordinates
-    This file needs to be of the form Gene, x-coordinate, y-coordinate.
+    This file needs to be of the form gene, x-coordinate, y-coordinate.
     The name of the headers are irrelevant, however their order needs to be kept.
     Negative coordinates are possible and the units do not matter. However, their magnitude 
     might have an influence on proper parameter values later on.
 
     +----------+-----------+-----------+
-    | Gene     |   x       |   y       |
+    | gene,    |   x,      |   y       |
     +----------+-----------+-----------+
-    | Gene A   |   0.5     |   1.3     |
+    | gene A,  |   0.5,    |   1.3     |
     +----------+-----------+-----------+
-    | Gene A   |   1.1     |   2.1     |
+    | gene A,  |   1.1,    |   2.1     |
     +----------+-----------+-----------+
-    | Gene B   |   0.4     |   0.5     |
+    | gene B,  |   0.4,    |   0.5     |
     +----------+-----------+-----------+
 
 Gene Signatures
-    This file should be a matrix of Cell types by Genes. 
-    The first column and row contains the names of Cell types and Genes, respectively. All the other cell values
+    This file should be a matrix of cell types by genes. 
+    The first column and row contains the names of cell types and genes, respectively. All the other cell values
     are gene scores ... TODO  how to define this ...
     This will later be used to assign each pixel to a cell type (or leave them unclassified)
-    based on the Kernel Density Estimation.
+    based on the kernel density estimation.
 
     +--------------+----------+-----------+-----------+
-    |              | Gene A   | Gene B    | Gene C    |
+    |       ,      | gene A,  | gene B,   | gene C    |
     +--------------+----------+-----------+-----------+
-    | Celltype A   |    0.5   |   -0.5    |   1.3     |
+    | cell type A, |    0.5,  |   -0.5,   |   1.3     |
     +--------------+----------+-----------+-----------+
-    | Celltype B   |    -0.2  |   1.1     |   2.1     |
+    | cell type B, |    -0.2, |   1.1,    |   2.1     |
     +--------------+----------+-----------+-----------+
-    | Celltype C   |    0.3   |   0.4     |   0.5     |
+    | cell type C, |    0.3,  |   0.4,    |   0.5     |
     +--------------+----------+-----------+-----------+
 
 
 .. note::
-    The name of the genes sre not relevant as there is no database used in the background.
+    The name of the genes need not be correct as there is no database used in the background.
     But remember that the gene names from the coordinates and the signatures need to be the same
-    (or at least the two sets of names must be at least partially overlapping).
+    (or more specifically the two sets of names must be partially overlapping).
 
 Once both files are loaded you can proceed with setting the parameters for your analysis.
 
 Parameters
 ===========
 
-For a deep understanding of the SSAM framework we would refer the user to the
+For a more detailed explanation of the SSAM framework we would refer the user to the
 `SSAM publication <https://www.nature.com/articles/s41467-021-23807-4>`__,
 however we will briefly describe the purpose and effect of the parameters
 that can be set by the user to obtain optimal results.
 
 Vector field width
     The vector field width defines the horizontal pixel count of the output images.
-    This is necessary as the KDE will be projected onto discrete locations (the pixels).
+    This is necessary as the kernel density estimation (KDE) will be projected onto 
+    discrete locations (the pixels).
 
     A higher value will result in higher resolution but also in increased processing time and memory
     as well as size of the output images.
 
 KDE kernel bandwidth (sigma)
-    The kernel bandwidth TODO definition?
+    SSAM-lite uses a Gaussian kernel and the kernel bandwidth defines the "range" of 
+    integration of data points (mRNA spots) for the KDE.
 
     A higher value will result in an increased smoothing of the mRNA density estimation.
 
 Cell assignment threshold
     This threshold is used to decide whether a pixel in the KDE projection belongs to
-    a cell or not. It is visualised in the parameter preview to help find an 
-    optimal value.
+    a cell or not. 
+    
+    As help to pick an optimal value you can check the KDE estimate (middle plot in the parameter preview)
+    to find the intensity that should serve as cutoff point.
 
 
 Each of the parameters can be set in their respective field and applied by hitting Enter.
@@ -129,7 +133,7 @@ Once it finished, the KDE estimates will be displayed in a plot (see example bel
 This step is the computationally most expensive and might tak a few minutes.
 
 .. note::
-    If you are using SSAM-lite-solo your Browser might warn you that it is being slowed down by the current site.
+    If you are using SSAM-lite-solo your browser might warn you that it is being slowed down by the current site.
     This is normal due to the heavy computation running in the background and can be ignored.
 
 .. image:: ../res/imgs/KDE.png
@@ -144,7 +148,7 @@ The inferred cell types will be displayed in a new plot.
   :width: 800
   :alt: Cell types inferred from KDE using the provided gene signatures
 
-If you are not content with the results you can go back to the parameters section
+If you are not satisfied with the results you can go back to the parameters section
 and refine those before rerunning the analysis.
 
 
@@ -153,4 +157,4 @@ Save results
 
 All plots are produced with `Plotly <https://plotly.com/>`__ and can be downloaded
 by hovering over the plot which triggers a legend to appear in the upper right corner,
-now click the Camera icon which lets you download the current plot as png file.
+now click the camera icon which lets you download the current plot as png file.
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
index 657f330..9572026 100644
--- a/docs/build/html/genindex.html
+++ b/docs/build/html/genindex.html
@@ -38,7 +38,6 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="quickstart.html">quickstart / tldr</a></li>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage.html">Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="solo_vs_server.html">Solo or Server?</a></li>
 </ul>
diff --git a/docs/build/html/index.html b/docs/build/html/index.html
index 34ff8ab..383df0f 100644
--- a/docs/build/html/index.html
+++ b/docs/build/html/index.html
@@ -40,7 +40,6 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="quickstart.html">quickstart / tldr</a></li>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage.html">Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="solo_vs_server.html">Solo or Server?</a></li>
 </ul>
@@ -73,8 +72,10 @@
 <h1>What is SSAM-lite?<a class="headerlink" href="#what-is-ssam-lite" title="Permalink to this headline"></a></h1>
 <p>SSAM-lite is a lightweight, browser-based implementation of the <a class="reference external" href="https://www.nature.com/articles/s41467-021-23807-4">SSAM framework</a>.
 It provides the functionality of SSAMs most popular and widely used features in a graphical user interface
-with a few functions added for convenience and ease of use.</p>
-<p>TODO what does SSAM do</p>
+with a few functions added for convenience and ease of use. It neiteher requires specialised computational experts
+nor hardware to handle and process data and thus can be run on a modest laptop.</p>
+<p>The SSAM framework allows for cell segmentation-free identification of cell-types by integrating prior knowledge of
+cell type-specific gene signatures with data from a variety of spatial in situ transcriptomics techniques.</p>
 <section id="citations">
 <h2>Citations<a class="headerlink" href="#citations" title="Permalink to this headline"></a></h2>
 <p>TODO please correct me!</p>
@@ -118,7 +119,6 @@ <h2>License<a class="headerlink" href="#license" title="Permalink to this headli
 <li class="toctree-l2"><a class="reference internal" href="installation.html#ssam-lite-server">SSAM-lite-server</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage.html">Usage</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="usage.html#open-ssam-lite">Open SSAM-lite</a></li>
 <li class="toctree-l2"><a class="reference internal" href="usage.html#navigation">Navigation</a></li>
diff --git a/docs/build/html/installation.html b/docs/build/html/installation.html
index 9f1a395..74b7094 100644
--- a/docs/build/html/installation.html
+++ b/docs/build/html/installation.html
@@ -18,7 +18,7 @@
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="Tutorial" href="tutorial.html" />
+    <link rel="next" title="Usage" href="usage.html" />
     <link rel="prev" title="quickstart / tldr" href="quickstart.html" /> 
 </head>
 
@@ -46,7 +46,6 @@
 <li class="toctree-l2"><a class="reference internal" href="#ssam-lite-server">SSAM-lite-server</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage.html">Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="solo_vs_server.html">Solo or Server?</a></li>
 </ul>
@@ -84,7 +83,7 @@ <h1>Installation<a class="headerlink" href="#installation" title="Permalink to t
 <section id="supported-browsers">
 <span id="id1"></span><h2>Supported Browsers<a class="headerlink" href="#supported-browsers" title="Permalink to this headline"></a></h2>
 <p>TODO
-We should add some stuff about requirments etc</p>
+We should add some stuff about requirements etc</p>
 </section>
 <section id="ssam-lite-solo">
 <h2>SSAM-lite-solo<a class="headerlink" href="#ssam-lite-solo" title="Permalink to this headline"></a></h2>
@@ -120,14 +119,14 @@ <h2>SSAM-lite-server<a class="headerlink" href="#ssam-lite-server" title="Permal
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda install flask numpy pandas
 </pre></div>
 </div>
-<dl class="simple">
-<dt>And start the server.</dt><dd><p>cd /ssamLiteDev/scripts/flask
-export FLASK_APP=run.py
-export FLASK_ENV=development
-flask run</p>
-</dd>
-</dl>
-<p>Open browser at 127.0.0.1:5000</p>
+<p>And start the server.</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> /ssamLiteDev/scripts/flask
+<span class="nb">export</span> <span class="nv">FLASK_APP</span><span class="o">=</span>run.py
+<span class="nb">export</span> <span class="nv">FLASK_ENV</span><span class="o">=</span>development
+flask run
+</pre></div>
+</div>
+<p>Type in the address bar of your browser: 127.0.0.1:5000</p>
 <p>This definitely needs to be explained.
 However, somebody with a little bit expertise should do this,
 most of it will be config dependent and people installing this will most likely know what they are doing!</p>
@@ -139,7 +138,7 @@ <h2>SSAM-lite-server<a class="headerlink" href="#ssam-lite-server" title="Permal
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="quickstart.html" class="btn btn-neutral float-left" title="quickstart / tldr" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="tutorial.html" class="btn btn-neutral float-right" title="Tutorial" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="usage.html" class="btn btn-neutral float-right" title="Usage" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>
diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv
index c3248bb..aff2de0 100644
--- a/docs/build/html/objects.inv
+++ b/docs/build/html/objects.inv
@@ -2,6 +2,5 @@
 # Project: SSAM-lite
 # Version: 
 # The remainder of this file is compressed using zlib.
-xڅ�1o� �w~R�Ҫk���:D��V#b��z�9Ǒ6��l�Hݎ���=Dg7�#=�5���e7��=A��Q,1�m
-��^�t^6��V�c��q�@�á�}�~Q�͝>�E�Ff�hةY����.��:}
-���
�˚���"�$	o5�}�0k�h��ӝ
��Ζ�0�۟�>{W�a%��J�xKR7�N�M��tG$�F�c��n>%5��:1�#9
��Yˋߧ�>���]��H��W��4
\ No newline at end of file
+xڅ�1O�0�w���`5������R�1Vn|J,�\�]
+���u�ش����=�n��,�ٛz�O���C/GoiTk�R�BE�7��i^��;�M���8jj՗����do��z12�%;y���?��,}�S�_�k?c� e�U�d�z�6(Fھ>��L4�ߙ�'MA3��?L��'�g����CU��$u��T��MO�HA��C����է��3�&��)o_�|�=��"��r
\ No newline at end of file
diff --git a/docs/build/html/search.html b/docs/build/html/search.html
index 35610d0..01e05bf 100644
--- a/docs/build/html/search.html
+++ b/docs/build/html/search.html
@@ -41,7 +41,6 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="quickstart.html">quickstart / tldr</a></li>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage.html">Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="solo_vs_server.html">Solo or Server?</a></li>
 </ul>
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index 2f4b4c7..9bdbc6e 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({docnames:["index","installation","quickstart","solo_vs_server","tutorial","usage"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":4,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,sphinx:56},filenames:["index.rst","installation.rst","quickstart.rst","solo_vs_server.rst","tutorial.rst","usage.rst"],objects:{},objnames:{},objtypes:{},terms:{"0":[1,5],"1":[1,5],"10":0,"1101":0,"127":[1,5],"2":[2,5],"2021":0,"3":5,"4":5,"5":5,"5000":[1,5],"8qxkgg16zelg6ya":1,"break":2,"default":[2,5],"do":[0,1,2,4,5],"ds\u00e4lifhsdf\u00e4lgh":[],"export":1,"function":0,"new":5,"public":5,"short":2,"switch":5,"while":1,A:[0,5],AND:0,AS:0,And:1,BE:0,BUT:0,But:5,By:5,FOR:0,For:[2,5],IF:[],IN:0,IS:0,If:[1,5],It:[0,5],NO:0,NOT:0,OF:0,OR:0,THE:0,TO:0,That:[1,2],The:[0,1,5],There:[],To:[1,5],WITH:0,Will:1,_:[],_solo_or_serv:[],abl:5,about:1,abov:0,action:0,activ:1,actual:5,ad:0,add:1,address:5,after:4,afterward:5,all:[0,1,5],almost:[1,5],also:5,an:[0,5],analysi:0,ani:[0,5],anywai:4,app:[],appear:5,appli:5,ar:[1,5],aris:0,asdha:[],assign:5,associ:0,author:0,b:5,back:5,background:5,bandwidth:5,bar:5,base:[0,5],basic:4,been:2,befor:5,being:5,belong:5,below:5,best:1,between:[4,5],biorxiv:0,bit:1,boettich:0,both:5,briefli:5,bring:5,browser:[0,5],button:5,c:[0,5],camera:5,can:[1,2,5],cd:1,cell:[2,5],celltyp:5,center:5,charg:0,choic:5,claim:0,click:[2,5],clone:1,column:5,com:1,come:1,compat:5,comput:5,computation:5,conda:1,condit:0,config:1,connect:[0,5],connet:[],contain:5,content:5,contract:0,conveni:0,coordin:[2,5],copi:0,copyright:0,corner:5,correct:[0,5],could:1,count:5,creat:1,csv:[2,5],current:5,damag:0,data:[0,1],databas:5,deal:0,decid:[1,5],deep:5,defin:5,definit:[1,5],densiti:[2,5],depend:[1,5],describ:5,develop:1,differ:[1,5],directli:5,directori:[2,5],discret:5,displai:5,distribut:0,dl:1,document:0,doe:0,doi:0,done:2,doubl:[2,5],down:[2,5],download:[1,2,5],dropbox:1,due:5,duh:2,e:5,each:5,eas:0,easi:2,easier:1,effect:5,eil:0,either:[1,5],enter:5,environ:1,estim:[2,5],etc:1,event:0,exampl:5,execut:5,expect:[],expens:5,experti:[],expertis:1,explain:1,explor:5,express:0,extract:[1,2],favourit:5,featur:0,few:[0,5],field:5,file:[0,1,5],find:5,finish:5,first:[0,1,5],fit:[0,1],flask:1,flask_app:1,flask_env:1,flavor:1,fly:2,follow:[0,1,5],form:5,format:5,forward:5,framework:[0,5],free:0,from:[0,1,2,5],furnish:0,further:2,furthermor:5,g:5,gene:5,gener:5,genet:1,get:[2,4,5],git:1,github:1,given:5,glanc:2,go:[1,2,5],grant:0,graphic:0,guid:1,ha:2,handl:1,happi:5,have:5,head:2,header:5,heavi:5,help:[1,4,5],here:2,herebi:0,higher:5,hit:[2,5],holder:0,horizont:5,hover:5,how:[1,2,5],howev:[1,5],html:[2,5],http:1,icon:5,ident:[1,5],ie:5,ignor:5,imag:5,implement:[0,1],impli:0,includ:0,increas:5,index:[2,5],infer:[2,5],influenc:5,input:5,instal:[0,4],interact:5,interfac:0,intuit:5,ip:5,irrelev:5,ishaqu:0,jump:5,just:2,kde:[2,5],kept:5,kernel:[2,5],kind:0,know:[1,2,4],label:[],later:5,least:5,leav:[2,5],legend:5,let:5,liabil:0,liabl:0,light:0,lightweight:0,like:1,limit:0,link:[],list:5,lite:[2,4],liter:1,littl:[1,2],load:5,local:5,locat:5,lot:[1,4],mackowiak:0,magnitud:5,matrix:5,matter:5,me:0,memori:5,merchant:0,merg:0,might:[2,5],min:2,minut:5,mit:0,modifi:0,modul:[],more:5,most:[0,1,5],mrna:5,mst:[],mueller:0,must:5,my:0,n:1,name:[1,5],nave:0,navig:0,necessari:5,need:[1,4,5],neg:5,new_sheet:1,next:[1,5],nikla:0,noninfring:0,normal:5,note:[],notic:0,now:[1,2,5],numpi:1,obtain:[0,5],obvious:2,onc:5,onli:[],onto:5,onyl:5,open:[0,1,2],optim:5,order:5,org:[],other:[0,5],otherwis:0,out:0,output:5,over:5,overlap:5,packag:1,page:[],panda:1,paper:[],paramet:[0,2],partial:5,particular:0,peopl:1,permiss:0,permit:0,person:0,pictur:[],pixel:5,place:1,pleas:0,plot:5,plotli:5,png:5,popular:0,port:5,portion:0,possibl:5,prefer:1,prepar:5,preview:5,proce:5,process:5,produc:5,project:5,proper:5,provid:[0,1],publish:0,purpos:[0,5],py:1,quick:2,quickstart:[0,4],quit:1,read:5,readi:1,refer:5,refernc:[],refin:5,relev:5,rememb:5,repositori:1,requir:[1,5],rerun:5,resolut:5,resolv:0,respect:5,respons:5,restrict:0,result:0,right:[0,5],roland:0,room:4,row:5,run:[1,2,5],s:[1,2],sahai:0,same:[2,5],sampl:2,save:0,score:5,script:1,scroll:[2,5],sdlfh:[],search:5,sebastian:0,sebastiantiesmey:[0,1],section:[2,5],see:5,select:[2,5],sell:0,server:0,set:[1,5],setup:5,shall:0,shashwat:0,should:[1,5],sigma:5,signatur:[1,2,5],singatur:1,site:5,size:5,skip:2,slow:5,smooth:5,so:[0,2],softwar:0,solo:[0,2],some:1,somebodi:1,spatial:0,sre:5,ssam:[2,4],ssamlit:1,ssamlitedev:1,start:[1,5],step:[2,5],stick:0,straight:[2,5],structur:5,stuff:1,subject:0,sublicens:0,subset:5,substanti:0,support:[0,5],tak:5,take:2,talk:5,tar:1,test:0,thei:1,them:[2,5],thi:[0,1,2,4,5],those:[2,5],threshold:5,tiesmey:0,time:[2,5],tldr:0,todo:[0,1,2,4,5],tool:5,top:5,tort:0,transcriptom:0,trigger:5,tune:5,tutori:0,two:[1,5],type:[2,5],unclassifi:5,understand:5,unit:5,until:5,unzip:[2,5],up:5,upload:5,upper:5,us:[0,2,5],usag:[0,1,4],user:[0,5],valu:[2,5],vector:5,veri:2,version:[1,5],visualis:5,wait:5,want:[2,5],warn:5,warranti:0,we:[0,1,2,4,5],web:[0,5],webapp:[],weight:0,well:5,what:[1,2],when:2,whether:[0,5],which:[1,5],who:2,whom:0,wide:0,width:5,window:5,without:0,workflow:4,would:5,www:1,x:5,xz:1,y:5,yaml:1,you:[1,4,5],your:[1,5],zip:[1,2]},titles:["What is SSAM-lite?","Installation","quickstart / tldr","Solo or Server?","Tutorial","Usage"],titleterms:{analysi:[2,5],browser:1,citat:0,content:0,data:[2,5],document:[],first:2,how:[],indic:[],instal:[1,2],licens:0,lite:[0,1,5],my:2,navig:5,open:5,paramet:5,quickstart:2,result:5,s:[],save:5,server:[1,3,5],solo:[1,3,5],ssam:[0,1,5],support:1,tabl:[],test:2,tldr:2,tutori:4,us:[],usag:5,welcom:[],what:0}})
\ No newline at end of file
+Search.setIndex({docnames:["index","installation","quickstart","solo_vs_server","usage"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":4,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,sphinx:56},filenames:["index.rst","installation.rst","quickstart.rst","solo_vs_server.rst","usage.rst"],objects:{},objnames:{},objtypes:{},terms:{"0":[1,4],"1":[1,4],"10":0,"1101":0,"127":[1,4],"2":[2,4],"2021":0,"3":4,"4":4,"5":4,"5000":[1,4],"8qxkgg16zelg6ya":1,"break":2,"default":[2,4],"do":[0,1,2,4],"ds\u00e4lifhsdf\u00e4lgh":[],"export":1,"function":0,"new":4,"public":4,"short":2,"switch":4,"while":1,A:[0,4],AND:0,AS:0,And:1,As:4,BE:0,BUT:0,But:4,By:4,FOR:0,For:[2,4],IF:[],IN:0,IS:0,If:[1,4],It:[0,4],NO:0,NOT:0,OF:0,OR:0,THE:0,TO:0,That:[1,2],The:[0,1,4],There:[],To:[1,4],WITH:0,Will:1,_:[],_solo_or_serv:[],abl:4,about:1,abov:0,action:0,activ:1,actual:4,ad:0,add:1,address:[1,4],after:[],afterward:4,all:[0,1,4],allow:0,almost:[1,4],also:4,an:[0,4],analysi:0,ani:[0,4],anywai:[],app:[],appear:4,appli:4,ar:[1,4],aris:0,asdha:[],assign:4,associ:0,author:0,b:4,back:4,background:4,bandwidth:4,bar:[1,4],base:[0,4],basic:[],been:2,befor:4,being:4,belong:4,below:4,best:1,between:4,biorxiv:0,bit:1,boettich:0,both:4,briefli:4,bring:4,browser:[0,4],button:4,c:[0,4],camera:4,can:[0,1,2,4],cd:1,cell:[0,2,4],celltyp:[],center:4,charg:0,check:4,choic:4,claim:0,click:[2,4],clone:1,column:4,com:1,come:1,compat:4,comput:[0,4],computation:4,conda:1,condit:0,config:1,connect:[0,4],connet:[],contain:4,content:[],contract:0,conveni:0,coordin:[2,4],copi:0,copyright:0,corner:4,correct:[0,4],could:1,count:4,creat:1,csv:[2,4],current:4,cutoff:4,damag:0,data:[0,1],databas:4,deal:0,decid:[1,4],deep:[],defin:4,definit:1,densiti:[2,4],depend:[1,4],describ:4,detail:4,develop:1,differ:[1,4],directli:4,directori:[2,4],discret:4,displai:4,distribut:0,dl:1,document:0,doe:[],doi:0,done:2,doubl:[2,4],down:[2,4],download:[1,2,4],dropbox:1,due:4,duh:2,e:4,each:4,eas:0,easi:2,easier:1,effect:4,eil:0,either:[1,4],enter:4,environ:1,estim:[2,4],etc:1,event:0,exampl:4,execut:4,expect:[],expens:4,expert:0,experti:[],expertis:1,explain:1,explan:4,explor:4,express:0,extract:[1,2],favourit:4,featur:0,few:[0,4],field:4,file:[0,1,4],find:4,finish:4,first:[0,1,4],fit:[0,1],flask:1,flask_app:1,flask_env:1,flavor:1,fly:2,follow:[0,1,4],form:4,format:4,forward:4,framework:[0,4],free:0,from:[0,1,2,4],furnish:0,further:2,furthermor:4,g:4,gaussian:4,gene:[0,4],gener:4,genet:1,get:[2,4],git:1,github:1,given:4,glanc:2,go:[1,2,4],grant:0,graphic:0,guid:1,ha:2,handl:[0,1],happi:4,hardwar:0,have:4,head:2,header:4,heavi:4,help:[1,4],here:2,herebi:0,higher:4,hit:[2,4],holder:0,horizont:4,hover:4,how:[1,2,4],howev:[1,4],html:[2,4],http:1,icon:4,ident:[1,4],identif:0,ie:4,ignor:4,imag:4,implement:[0,1],impli:0,includ:0,increas:4,index:[2,4],infer:[2,4],influenc:4,input:4,instal:0,integr:[0,4],intens:4,interact:4,interfac:0,intuit:4,ip:4,irrelev:4,ishaqu:0,jump:4,just:2,kde:[2,4],kept:4,kernel:[2,4],kind:0,know:[1,2],knowledg:0,label:[],laptop:0,later:4,least:[],leav:[2,4],legend:4,let:4,liabil:0,liabl:0,light:0,lightweight:0,like:1,limit:0,link:[],list:4,lite:2,liter:1,littl:[1,2],load:4,local:4,locat:4,lot:1,mackowiak:0,magnitud:4,matrix:4,matter:4,me:0,memori:4,merchant:0,merg:0,middl:4,might:[2,4],min:2,minut:4,mit:0,modest:0,modifi:0,modul:[],more:4,most:[0,1,4],mrna:4,mst:[],mueller:0,must:4,my:0,n:1,name:[1,4],nave:0,navig:0,necessari:4,need:[1,4],neg:4,neiteh:0,new_sheet:1,next:[1,4],nikla:0,noninfring:0,nor:0,normal:4,note:[],notic:0,now:[1,2,4],numpi:1,obtain:[0,4],obvious:2,onc:4,onli:4,onto:4,onyl:[],open:[0,2],optim:4,order:4,org:[],other:[0,4],otherwis:0,out:0,output:4,over:4,overlap:4,packag:1,page:[],panda:1,paper:[],paramet:[0,2],partial:4,particular:0,peopl:1,permiss:0,permit:0,person:0,pick:4,pictur:[],pixel:4,place:1,pleas:0,plot:4,plotli:4,png:4,point:4,popular:0,port:4,portion:0,possibl:4,prefer:1,prepar:4,preview:4,prior:0,proce:4,process:[0,4],produc:4,project:4,proper:4,provid:[0,1],publish:0,purpos:[0,4],py:1,quick:2,quickstart:0,quit:1,rang:4,read:4,readi:1,refer:4,refernc:[],refin:4,relev:[],rememb:4,repositori:1,requir:[0,1,4],rerun:4,resolut:4,resolv:0,respect:4,respons:4,restrict:0,result:0,right:[0,4],roland:0,room:[],row:4,run:[0,1,2,4],s:[1,2],sahai:0,same:[2,4],sampl:2,satisfi:4,save:0,score:4,script:1,scroll:[2,4],sdlfh:[],search:4,sebastian:0,sebastiantiesmey:[0,1],section:[2,4],see:4,segment:0,select:[2,4],sell:0,serv:4,server:0,set:[1,4],setup:4,shall:0,shashwat:0,should:[1,4],sigma:4,signatur:[0,1,2,4],singatur:1,site:4,situ:0,size:4,skip:2,slow:4,smooth:4,so:[0,2],softwar:0,solo:[0,2],some:1,somebodi:1,spatial:0,specialis:0,specif:[0,4],spot:4,sre:[],ssam:2,ssamlit:1,ssamlitedev:1,start:[1,4],step:[2,4],stick:0,straight:[2,4],structur:4,stuff:1,subject:0,sublicens:0,subset:4,substanti:0,support:[0,4],tak:4,take:2,talk:4,tar:1,techniqu:0,test:0,thei:1,them:[2,4],thi:[0,1,2,4],those:[2,4],threshold:4,thu:0,tiesmey:0,time:[2,4],tldr:0,todo:[0,1,2,4],tool:4,top:4,tort:0,transcriptom:0,trigger:4,tune:4,tutori:[],two:[1,4],type:[0,1,2,4],unclassifi:4,understand:[],unit:4,until:4,unzip:[2,4],up:4,upload:4,upper:4,us:[0,2,4],usag:[0,1],user:[0,4],valu:[2,4],varieti:0,vector:4,veri:2,version:[1,4],visualis:[],wait:4,want:[2,4],warn:4,warranti:0,we:[0,1,2,4],web:[0,4],webapp:[],weight:0,well:4,what:[1,2],when:2,whether:[0,4],which:[1,4],who:2,whom:0,wide:0,width:4,window:4,without:0,workflow:[],would:4,www:1,x:4,xz:1,y:4,yaml:1,you:[1,4],your:[1,4],zip:[1,2]},titles:["What is SSAM-lite?","Installation","quickstart / tldr","Solo or Server?","Usage"],titleterms:{analysi:[2,4],browser:1,citat:0,content:0,data:[2,4],document:[],first:2,how:[],indic:[],instal:[1,2],licens:0,lite:[0,1,4],my:2,navig:4,open:4,paramet:4,quickstart:2,result:4,s:[],save:4,server:[1,3,4],solo:[1,3,4],ssam:[0,1,4],support:1,tabl:[],test:2,tldr:2,tutori:[],us:[],usag:4,welcom:[],what:0}})
\ No newline at end of file
diff --git a/docs/build/html/tutorial.html b/docs/build/html/tutorial.html
deleted file mode 100644
index ae725d7..0000000
--- a/docs/build/html/tutorial.html
+++ /dev/null
@@ -1,111 +0,0 @@
-<!DOCTYPE html>
-<html class="writer-html5" lang="en" >
-<head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
-
-  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Tutorial &mdash; SSAM-lite 0.1 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
-  <!--[if lt IE 9]>
-    <script src="_static/js/html5shiv.min.js"></script>
-  <![endif]-->
-  
-        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
-        <script src="_static/jquery.js"></script>
-        <script src="_static/underscore.js"></script>
-        <script src="_static/doctools.js"></script>
-    <script src="_static/js/theme.js"></script>
-    <link rel="index" title="Index" href="genindex.html" />
-    <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="Usage" href="usage.html" />
-    <link rel="prev" title="Installation" href="installation.html" /> 
-</head>
-
-<body class="wy-body-for-nav"> 
-  <div class="wy-grid-for-nav">
-    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
-      <div class="wy-side-scroll">
-        <div class="wy-side-nav-search" >
-            <a href="index.html" class="icon icon-home"> SSAM-lite
-          </a>
-<div role="search">
-  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
-    <input type="hidden" name="check_keywords" value="yes" />
-    <input type="hidden" name="area" value="default" />
-  </form>
-</div>
-        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
-<ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="quickstart.html">quickstart / tldr</a></li>
-<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="#">Tutorial</a></li>
-<li class="toctree-l1"><a class="reference internal" href="usage.html">Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="solo_vs_server.html">Solo or Server?</a></li>
-</ul>
-
-        </div>
-      </div>
-    </nav>
-
-    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
-          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="index.html">SSAM-lite</a>
-      </nav>
-
-      <div class="wy-nav-content">
-        <div class="rst-content">
-          <div role="navigation" aria-label="Page navigation">
-  <ul class="wy-breadcrumbs">
-      <li><a href="index.html" class="icon icon-home"></a> &raquo;</li>
-      <li>Tutorial</li>
-      <li class="wy-breadcrumbs-aside">
-            <a href="_sources/tutorial.rst.txt" rel="nofollow"> View page source</a>
-      </li>
-  </ul>
-  <hr/>
-</div>
-          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
-           <div itemprop="articleBody">
-             
-  <section id="tutorial">
-<h1>Tutorial<a class="headerlink" href="#tutorial" title="Permalink to this headline"></a></h1>
-<p>TODO do we need a tutorial? there is not a lot of room between the quickstart and the usage anyway?</p>
-<p>After installation of SSAM-lite, this tutorial will help you get to
-know the basic workflow of</p>
-</section>
-
-
-           </div>
-          </div>
-          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="installation.html" class="btn btn-neutral float-left" title="Installation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="usage.html" class="btn btn-neutral float-right" title="Usage" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
-    </div>
-
-  <hr/>
-
-  <div role="contentinfo">
-    <p>&#169; Copyright 2021, Niklas Müller-Bötticher ans Shashwat Sahay.</p>
-  </div>
-
-  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
-    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
-    provided by <a href="https://readthedocs.org">Read the Docs</a>.
-   
-
-</footer>
-        </div>
-      </div>
-    </section>
-  </div>
-  <script>
-      jQuery(function () {
-          SphinxRtdTheme.Navigation.enable(true);
-      });
-  </script> 
-
-</body>
-</html>
\ No newline at end of file
diff --git a/docs/build/html/usage.html b/docs/build/html/usage.html
index f1b1d8f..a3aa70e 100644
--- a/docs/build/html/usage.html
+++ b/docs/build/html/usage.html
@@ -19,7 +19,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Solo or Server?" href="solo_vs_server.html" />
-    <link rel="prev" title="Tutorial" href="tutorial.html" /> 
+    <link rel="prev" title="Installation" href="installation.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -41,7 +41,6 @@
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="quickstart.html">quickstart / tldr</a></li>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Usage</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#open-ssam-lite">Open SSAM-lite</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#ssam-lite-solo">SSAM-lite-solo</a></li>
@@ -91,14 +90,14 @@ <h2>Open SSAM-lite<a class="headerlink" href="#open-ssam-lite" title="Permalink
 <em>solo</em> or <em>server</em> version. However, the usage afterwards will be (almost) identical.</p>
 <section id="ssam-lite-solo">
 <h3>SSAM-lite-solo<a class="headerlink" href="#ssam-lite-solo" title="Permalink to this headline"></a></h3>
-<p>SSAM-lite-solo runs locally on your computer. It is executed by your Browser
-and to open it you onyl need to navigate to the unzipped SSAM-lite directory
-and double-click the <em>index.html</em> to open it in your default Web Browser.</p>
+<p>SSAM-lite-solo runs locally on your computer. It is executed by your browser
+and to open it you only need to navigate to the unzipped SSAM-lite directory
+and double-click the <em>index.html</em> and it will start in your default web browser.</p>
 </section>
 <section id="ssam-lite-server">
 <h3>SSAM-lite-server<a class="headerlink" href="#ssam-lite-server" title="Permalink to this headline"></a></h3>
-<p>To connect to SSAM-lite-server, you will need to to open your favourite Web Browser (not IE)
-and enter the correct IP address and port in the form {ip}:{port} (e.g. 127.0.0.1:5000).
+<p>To connect to SSAM-lite-server, you will need to to open your favourite web browser (not IE)
+and type the correct IP address and port in the form {ip}:{port} (e.g. 127.0.0.1:5000) into the address bar.
 However, the IP and port depends on your local setup. Talk to your responsible SSAM-lite coordinator.</p>
 </section>
 </section>
@@ -111,12 +110,12 @@ <h2>Navigation<a class="headerlink" href="#navigation" title="Permalink to this
 </section>
 <section id="data">
 <h2>Data<a class="headerlink" href="#data" title="Permalink to this headline"></a></h2>
-<p>The Data will be uploaded in the <strong>Data Center</strong> section of the tool. By clicking the “Coordinates”
+<p>The data will be uploaded in the <strong>Data Center</strong> section of the tool. By clicking the “Coordinates”
 or “Signatures” button and selecting the correct files.
 To be able to use SSAM-lite you need to prepare your data in csv format.
 Two input files are required and must be structured as follows:</p>
 <dl>
-<dt>mRNA Coordinates</dt><dd><p>This file needs to be of the form Gene, x-coordinate, y-coordinate.
+<dt>mRNA Coordinates</dt><dd><p>This file needs to be of the form gene, x-coordinate, y-coordinate.
 The name of the headers are irrelevant, however their order needs to be kept.
 Negative coordinates are possible and the units do not matter. However, their magnitude
 might have an influence on proper parameter values later on.</p>
@@ -127,30 +126,30 @@ <h2>Data<a class="headerlink" href="#data" title="Permalink to this headline">
 <col style="width: 34%" />
 </colgroup>
 <tbody>
-<tr class="row-odd"><td><p>Gene</p></td>
-<td><p>x</p></td>
+<tr class="row-odd"><td><p>gene,</p></td>
+<td><p>x,</p></td>
 <td><p>y</p></td>
 </tr>
-<tr class="row-even"><td><p>Gene A</p></td>
-<td><p>0.5</p></td>
+<tr class="row-even"><td><p>gene A,</p></td>
+<td><p>0.5,</p></td>
 <td><p>1.3</p></td>
 </tr>
-<tr class="row-odd"><td><p>Gene A</p></td>
-<td><p>1.1</p></td>
+<tr class="row-odd"><td><p>gene A,</p></td>
+<td><p>1.1,</p></td>
 <td><p>2.1</p></td>
 </tr>
-<tr class="row-even"><td><p>Gene B</p></td>
-<td><p>0.4</p></td>
+<tr class="row-even"><td><p>gene B,</p></td>
+<td><p>0.4,</p></td>
 <td><p>0.5</p></td>
 </tr>
 </tbody>
 </table>
 </dd>
-<dt>Gene Signatures</dt><dd><p>This file should be a matrix of Cell types by Genes.
-The first column and row contains the names of Cell types and Genes, respectively. All the other cell values
+<dt>Gene Signatures</dt><dd><p>This file should be a matrix of cell types by genes.
+The first column and row contains the names of cell types and genes, respectively. All the other cell values
 are gene scores … TODO  how to define this …
 This will later be used to assign each pixel to a cell type (or leave them unclassified)
-based on the Kernel Density Estimation.</p>
+based on the kernel density estimation.</p>
 <table class="docutils align-default">
 <colgroup>
 <col style="width: 30%" />
@@ -159,24 +158,24 @@ <h2>Data<a class="headerlink" href="#data" title="Permalink to this headline">
 <col style="width: 24%" />
 </colgroup>
 <tbody>
-<tr class="row-odd"><td></td>
-<td><p>Gene A</p></td>
-<td><p>Gene B</p></td>
-<td><p>Gene C</p></td>
+<tr class="row-odd"><td><p>,</p></td>
+<td><p>gene A,</p></td>
+<td><p>gene B,</p></td>
+<td><p>gene C</p></td>
 </tr>
-<tr class="row-even"><td><p>Celltype A</p></td>
-<td><p>0.5</p></td>
-<td><p>-0.5</p></td>
+<tr class="row-even"><td><p>cell type A,</p></td>
+<td><p>0.5,</p></td>
+<td><p>-0.5,</p></td>
 <td><p>1.3</p></td>
 </tr>
-<tr class="row-odd"><td><p>Celltype B</p></td>
-<td><p>-0.2</p></td>
-<td><p>1.1</p></td>
+<tr class="row-odd"><td><p>cell type B,</p></td>
+<td><p>-0.2,</p></td>
+<td><p>1.1,</p></td>
 <td><p>2.1</p></td>
 </tr>
-<tr class="row-even"><td><p>Celltype C</p></td>
-<td><p>0.3</p></td>
-<td><p>0.4</p></td>
+<tr class="row-even"><td><p>cell type C,</p></td>
+<td><p>0.3,</p></td>
+<td><p>0.4,</p></td>
 <td><p>0.5</p></td>
 </tr>
 </tbody>
@@ -185,30 +184,33 @@ <h2>Data<a class="headerlink" href="#data" title="Permalink to this headline">
 </dl>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
-<p>The name of the genes sre not relevant as there is no database used in the background.
+<p>The name of the genes need not be correct as there is no database used in the background.
 But remember that the gene names from the coordinates and the signatures need to be the same
-(or at least the two sets of names must be at least partially overlapping).</p>
+(or more specifically the two sets of names must be partially overlapping).</p>
 </div>
 <p>Once both files are loaded you can proceed with setting the parameters for your analysis.</p>
 </section>
 <section id="parameters">
 <h2>Parameters<a class="headerlink" href="#parameters" title="Permalink to this headline"></a></h2>
-<p>For a deep understanding of the SSAM framework we would refer the user to the
+<p>For a more detailed explanation of the SSAM framework we would refer the user to the
 <a class="reference external" href="https://www.nature.com/articles/s41467-021-23807-4">SSAM publication</a>,
 however we will briefly describe the purpose and effect of the parameters
 that can be set by the user to obtain optimal results.</p>
 <dl>
 <dt>Vector field width</dt><dd><p>The vector field width defines the horizontal pixel count of the output images.
-This is necessary as the KDE will be projected onto discrete locations (the pixels).</p>
+This is necessary as the kernel density estimation (KDE) will be projected onto
+discrete locations (the pixels).</p>
 <p>A higher value will result in higher resolution but also in increased processing time and memory
 as well as size of the output images.</p>
 </dd>
-<dt>KDE kernel bandwidth (sigma)</dt><dd><p>The kernel bandwidth TODO definition?</p>
+<dt>KDE kernel bandwidth (sigma)</dt><dd><p>SSAM-lite uses a Gaussian kernel and the kernel bandwidth defines the “range” of
+integration of data points (mRNA spots) for the KDE.</p>
 <p>A higher value will result in an increased smoothing of the mRNA density estimation.</p>
 </dd>
 <dt>Cell assignment threshold</dt><dd><p>This threshold is used to decide whether a pixel in the KDE projection belongs to
-a cell or not. It is visualised in the parameter preview to help find an
-optimal value.</p>
+a cell or not.</p>
+<p>As help to pick an optimal value you can check the KDE estimate (middle plot in the parameter preview)
+to find the intensity that should serve as cutoff point.</p>
 </dd>
 </dl>
 <p>Each of the parameters can be set in their respective field and applied by hitting Enter.
@@ -226,7 +228,7 @@ <h2>Analysis<a class="headerlink" href="#analysis" title="Permalink to this head
 This step is the computationally most expensive and might tak a few minutes.</p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
-<p>If you are using SSAM-lite-solo your Browser might warn you that it is being slowed down by the current site.
+<p>If you are using SSAM-lite-solo your browser might warn you that it is being slowed down by the current site.
 This is normal due to the heavy computation running in the background and can be ignored.</p>
 </div>
 <a class="reference internal image-reference" href="_images/KDE.png"><img alt="KDE estimation given the previously set parameters" src="_images/KDE.png" style="width: 800px;" /></a>
@@ -234,14 +236,14 @@ <h2>Analysis<a class="headerlink" href="#analysis" title="Permalink to this head
 Scroll down to “Step 2: Cell Assignments” and click on “Infer Cell Types”.
 The inferred cell types will be displayed in a new plot.</p>
 <a class="reference internal image-reference" href="_images/inferredCelltypes.png"><img alt="Cell types inferred from KDE using the provided gene signatures" src="_images/inferredCelltypes.png" style="width: 800px;" /></a>
-<p>If you are not content with the results you can go back to the parameters section
+<p>If you are not satisfied with the results you can go back to the parameters section
 and refine those before rerunning the analysis.</p>
 </section>
 <section id="save-results">
 <h2>Save results<a class="headerlink" href="#save-results" title="Permalink to this headline"></a></h2>
 <p>All plots are produced with <a class="reference external" href="https://plotly.com/">Plotly</a> and can be downloaded
 by hovering over the plot which triggers a legend to appear in the upper right corner,
-now click the Camera icon which lets you download the current plot as png file.</p>
+now click the camera icon which lets you download the current plot as png file.</p>
 </section>
 </section>
 
@@ -249,7 +251,7 @@ <h2>Save results<a class="headerlink" href="#save-results" title="Permalink to t
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="tutorial.html" class="btn btn-neutral float-left" title="Tutorial" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="installation.html" class="btn btn-neutral float-left" title="Installation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="solo_vs_server.html" class="btn btn-neutral float-right" title="Solo or Server?" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 06b4c04..a7d27a3 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -8,11 +8,11 @@ What is SSAM-lite?
 
 SSAM-lite is a lightweight, browser-based implementation of the `SSAM framework <https://www.nature.com/articles/s41467-021-23807-4>`__.
 It provides the functionality of SSAMs most popular and widely used features in a graphical user interface
-with a few functions added for convenience and ease of use.
-
-
-TODO what does SSAM do
+with a few functions added for convenience and ease of use. It neiteher requires specialised computational experts 
+nor hardware to handle and process data and thus can be run on a modest laptop.
 
+The SSAM framework allows for cell segmentation-free identification of cell-types by integrating prior knowledge of 
+cell type-specific gene signatures with data from a variety of spatial in situ transcriptomics techniques.
 
 Citations
 =================
@@ -60,6 +60,5 @@ SOFTWARE.
 
    quickstart
    installation
-   tutorial
    usage
    solo_vs_server
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
index c1c0179..f60d27a 100644
--- a/docs/source/installation.rst
+++ b/docs/source/installation.rst
@@ -14,7 +14,7 @@ Supported Browsers
 ==================
 
 TODO
-We should add some stuff about requirments etc
+We should add some stuff about requirements etc
 
 
 SSAM-lite-solo
@@ -27,6 +27,7 @@ The installation of SSAM-lite-solo could not be easier. You either clone the
 
    git clone https://github.com/sebastiantiesmeyer/ssamLite
 
+
 or download it as zip-file from GitHub and then extract it.
 
 That is literally all, you are ready to go.
@@ -45,6 +46,7 @@ To install SSAM-lite-server you first need to clone the
 
     git clone https://github.com/sebastiantiesmeyer/ssamLiteDev
 
+
 How to handle signatures ????
 Download singatures: https://www.dropbox.com/s/8qxkgg16zelg6ya/new_sheet.tar.xz?dl=0
 Place signatures in data/genetics/ ???
@@ -56,23 +58,30 @@ Next we create a ``conda`` environment (TODO we should provide a yaml?) and acti
     conda create -n flask
     conda activate flask
 
+
 .. note::
 
     You can set the environment name to your preferences.
 
+
 Now we need to install some dependencies. TODO should we provide versions of the packages?
 
 .. code-block:: bash
 
     conda install flask numpy pandas
 
+
 And start the server.
+
+.. code-block:: bash
+
     cd /ssamLiteDev/scripts/flask
     export FLASK_APP=run.py
     export FLASK_ENV=development
     flask run
 
-Open browser at 127.0.0.1:5000
+
+Type in the address bar of your browser: 127.0.0.1:5000
 
 This definitely needs to be explained.
 However, somebody with a little bit expertise should do this,
diff --git a/docs/source/tutorial.rst b/docs/source/tutorial.rst
deleted file mode 100644
index fa61da1..0000000
--- a/docs/source/tutorial.rst
+++ /dev/null
@@ -1,10 +0,0 @@
-########
-Tutorial
-########
-
-
-TODO do we need a tutorial? there is not a lot of room between the quickstart and the usage anyway?
-
-After installation of SSAM-lite, this tutorial will help you get to
-know the basic workflow of 
-
diff --git a/docs/source/usage.rst b/docs/source/usage.rst
index d9e2918..e565068 100644
--- a/docs/source/usage.rst
+++ b/docs/source/usage.rst
@@ -12,15 +12,15 @@ read :ref:`supported-browsers`. Connecting to SSAM-lite depends on whether you w
 SSAM-lite-solo
 --------------
 
-SSAM-lite-solo runs locally on your computer. It is executed by your Browser
-and to open it you onyl need to navigate to the unzipped SSAM-lite directory
-and double-click the *index.html* to open it in your default Web Browser.
+SSAM-lite-solo runs locally on your computer. It is executed by your browser
+and to open it you only need to navigate to the unzipped SSAM-lite directory
+and double-click the *index.html* and it will start in your default web browser.
 
 SSAM-lite-server
 ----------------
 
-To connect to SSAM-lite-server, you will need to to open your favourite Web Browser (not IE)
-and enter the correct IP address and port in the form {ip}:{port} (e.g. 127.0.0.1:5000).
+To connect to SSAM-lite-server, you will need to to open your favourite web browser (not IE)
+and type the correct IP address and port in the form {ip}:{port} (e.g. 127.0.0.1:5000) into the address bar.
 However, the IP and port depends on your local setup. Talk to your responsible SSAM-lite coordinator.
 
 Navigation
@@ -36,76 +36,80 @@ by uploading your data.
 Data
 ===========
 
-The Data will be uploaded in the **Data Center** section of the tool. By clicking the "Coordinates" 
+The data will be uploaded in the **Data Center** section of the tool. By clicking the "Coordinates" 
 or "Signatures" button and selecting the correct files.
 To be able to use SSAM-lite you need to prepare your data in csv format.
 Two input files are required and must be structured as follows:
 
 mRNA Coordinates
-    This file needs to be of the form Gene, x-coordinate, y-coordinate.
+    This file needs to be of the form gene, x-coordinate, y-coordinate.
     The name of the headers are irrelevant, however their order needs to be kept.
     Negative coordinates are possible and the units do not matter. However, their magnitude 
     might have an influence on proper parameter values later on.
 
     +----------+-----------+-----------+
-    | Gene     |   x       |   y       |
+    | gene,    |   x,      |   y       |
     +----------+-----------+-----------+
-    | Gene A   |   0.5     |   1.3     |
+    | gene A,  |   0.5,    |   1.3     |
     +----------+-----------+-----------+
-    | Gene A   |   1.1     |   2.1     |
+    | gene A,  |   1.1,    |   2.1     |
     +----------+-----------+-----------+
-    | Gene B   |   0.4     |   0.5     |
+    | gene B,  |   0.4,    |   0.5     |
     +----------+-----------+-----------+
 
 Gene Signatures
-    This file should be a matrix of Cell types by Genes. 
-    The first column and row contains the names of Cell types and Genes, respectively. All the other cell values
+    This file should be a matrix of cell types by genes. 
+    The first column and row contains the names of cell types and genes, respectively. All the other cell values
     are gene scores ... TODO  how to define this ...
     This will later be used to assign each pixel to a cell type (or leave them unclassified)
-    based on the Kernel Density Estimation.
+    based on the kernel density estimation.
 
     +--------------+----------+-----------+-----------+
-    |              | Gene A   | Gene B    | Gene C    |
+    |       ,      | gene A,  | gene B,   | gene C    |
     +--------------+----------+-----------+-----------+
-    | Celltype A   |    0.5   |   -0.5    |   1.3     |
+    | cell type A, |    0.5,  |   -0.5,   |   1.3     |
     +--------------+----------+-----------+-----------+
-    | Celltype B   |    -0.2  |   1.1     |   2.1     |
+    | cell type B, |    -0.2, |   1.1,    |   2.1     |
     +--------------+----------+-----------+-----------+
-    | Celltype C   |    0.3   |   0.4     |   0.5     |
+    | cell type C, |    0.3,  |   0.4,    |   0.5     |
     +--------------+----------+-----------+-----------+
 
 
 .. note::
-    The name of the genes sre not relevant as there is no database used in the background.
+    The name of the genes need not be correct as there is no database used in the background.
     But remember that the gene names from the coordinates and the signatures need to be the same
-    (or at least the two sets of names must be at least partially overlapping).
+    (or more specifically the two sets of names must be partially overlapping).
 
 Once both files are loaded you can proceed with setting the parameters for your analysis.
 
 Parameters
 ===========
 
-For a deep understanding of the SSAM framework we would refer the user to the
+For a more detailed explanation of the SSAM framework we would refer the user to the
 `SSAM publication <https://www.nature.com/articles/s41467-021-23807-4>`__,
 however we will briefly describe the purpose and effect of the parameters
 that can be set by the user to obtain optimal results.
 
 Vector field width
     The vector field width defines the horizontal pixel count of the output images.
-    This is necessary as the KDE will be projected onto discrete locations (the pixels).
+    This is necessary as the kernel density estimation (KDE) will be projected onto 
+    discrete locations (the pixels).
 
     A higher value will result in higher resolution but also in increased processing time and memory
     as well as size of the output images.
 
 KDE kernel bandwidth (sigma)
-    The kernel bandwidth TODO definition?
+    SSAM-lite uses a Gaussian kernel and the kernel bandwidth defines the "range" of 
+    integration of data points (mRNA spots) for the KDE.
 
     A higher value will result in an increased smoothing of the mRNA density estimation.
 
 Cell assignment threshold
     This threshold is used to decide whether a pixel in the KDE projection belongs to
-    a cell or not. It is visualised in the parameter preview to help find an 
-    optimal value.
+    a cell or not. 
+    
+    As help to pick an optimal value you can check the KDE estimate (middle plot in the parameter preview)
+    to find the intensity that should serve as cutoff point.
 
 
 Each of the parameters can be set in their respective field and applied by hitting Enter.
@@ -129,7 +133,7 @@ Once it finished, the KDE estimates will be displayed in a plot (see example bel
 This step is the computationally most expensive and might tak a few minutes.
 
 .. note::
-    If you are using SSAM-lite-solo your Browser might warn you that it is being slowed down by the current site.
+    If you are using SSAM-lite-solo your browser might warn you that it is being slowed down by the current site.
     This is normal due to the heavy computation running in the background and can be ignored.
 
 .. image:: ../res/imgs/KDE.png
@@ -144,7 +148,7 @@ The inferred cell types will be displayed in a new plot.
   :width: 800
   :alt: Cell types inferred from KDE using the provided gene signatures
 
-If you are not content with the results you can go back to the parameters section
+If you are not satisfied with the results you can go back to the parameters section
 and refine those before rerunning the analysis.
 
 
@@ -153,4 +157,4 @@ Save results
 
 All plots are produced with `Plotly <https://plotly.com/>`__ and can be downloaded
 by hovering over the plot which triggers a legend to appear in the upper right corner,
-now click the Camera icon which lets you download the current plot as png file.
+now click the camera icon which lets you download the current plot as png file.

From 920fdb250844460594fd3fae69180fcaea04729d Mon Sep 17 00:00:00 2001
From: niklasmueboe <muellni@pmn-bih-dh-12.charite.de>
Date: Mon, 20 Sep 2021 11:25:31 +0200
Subject: [PATCH 2/2] tiny update to #22 before moving repo

---
 docs/source/quickstart.rst | 7 ++++++-
 docs/source/usage.rst      | 3 +++
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/docs/source/quickstart.rst b/docs/source/quickstart.rst
index 876f199..8668928 100644
--- a/docs/source/quickstart.rst
+++ b/docs/source/quickstart.rst
@@ -20,7 +20,12 @@ to download SSAM-lite-solo as zip, and extract it.
 Test data
 =========
 
-Download the test data from ..... TODO
+Download the test data from Zenodo via 
+
+.. code-block:: bash
+
+   wget https://zenodo.org/record/ .... TODO
+
 
 
 My first analysis
diff --git a/docs/source/usage.rst b/docs/source/usage.rst
index e565068..f919c77 100644
--- a/docs/source/usage.rst
+++ b/docs/source/usage.rst
@@ -2,6 +2,9 @@
 Usage
 ####################
 
+If you want to follow our usage guide along with some sample data you can download a sample data set from
+Zenodo (https://zenodo.org/doi????).
+
 Open SSAM-lite
 ==============