From 7782a90755f58b9fe9720c662cf6b35ea97de306 Mon Sep 17 00:00:00 2001
From: Antoine Weisrock <antoine.weisrock@gmail.com>
Date: Mon, 2 Oct 2023 10:34:03 +0200
Subject: [PATCH 1/4] perf: make segmentation sharper

nuclei detection is now sharper after adjusting the parameters of the underlying AI module

Signed-off-by: Antoine Weisrock <antoine.weisrock@gmail.com>
---
 src/myofinder/image_segmentation.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/myofinder/image_segmentation.py b/src/myofinder/image_segmentation.py
index 7cdffcb..a2da762 100644
--- a/src/myofinder/image_segmentation.py
+++ b/src/myofinder/image_segmentation.py
@@ -67,16 +67,16 @@ def __call__(self,
 
         del image
 
-        # Default parameters
-        radius = 10
-        maxima_threshold = 0.1
-        interior_threshold = 0.01
+        # Segmentation parameters
+        radius = 2
+        maxima_threshold = 0.05
+        interior_threshold = 0.3
         maxima_smooth = 0
-        interior_smooth = 0
+        interior_smooth = 2
         maxima_index = 0
         interior_index = -1
         label_erosion = 0
-        fill_holes_threshold = 0
+        fill_holes_threshold = 15
         pixel_expansion = None
         maxima_algorith = 'h_maxima'
 

From 34877a4b510ca2ac8619147f3cd6b5e9f3099c35 Mon Sep 17 00:00:00 2001
From: Antoine Weisrock <antoine.weisrock@gmail.com>
Date: Mon, 2 Oct 2023 10:39:11 +0200
Subject: [PATCH 2/4] build: update the version to 1.0.5

---
 src/myofinder/__version__.py              | 2 +-
 src/windows_installer/config.aip          | 2 +-
 src/windows_installer/start_myofinder.bat | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/myofinder/__version__.py b/src/myofinder/__version__.py
index 9fb71f3..8d7414f 100644
--- a/src/myofinder/__version__.py
+++ b/src/myofinder/__version__.py
@@ -1,3 +1,3 @@
 # coding: utf-8
 
-__version__ = '1.0.4'
+__version__ = '1.0.5'
diff --git a/src/windows_installer/config.aip b/src/windows_installer/config.aip
index e391bf3..8def804 100644
--- a/src/windows_installer/config.aip
+++ b/src/windows_installer/config.aip
@@ -15,7 +15,7 @@
     <ROW Property="ProductCode" Value="1033:{BFA51019-B48F-475B-B8BB-E2F14499079C} " Type="16"/>
     <ROW Property="ProductLanguage" Value="1033"/>
     <ROW Property="ProductName" Value="MyoFInDer"/>
-    <ROW Property="ProductVersion" Value="1.0.4" Options="32"/>
+    <ROW Property="ProductVersion" Value="1.0.5" Options="32"/>
     <ROW Property="SecureCustomProperties" Value="OLDPRODUCTS;AI_NEWERPRODUCTFOUND"/>
     <ROW Property="UpgradeCode" Value="{CE95562D-8E91-4ED9-B26E-5638FFE5C0B0}"/>
     <ROW Property="WindowsType9X" MultiBuildValue="DefaultBuild:Windows 9x/ME" ValueLocId="-"/>
diff --git a/src/windows_installer/start_myofinder.bat b/src/windows_installer/start_myofinder.bat
index 0432ed4..81f8ebd 100644
--- a/src/windows_installer/start_myofinder.bat
+++ b/src/windows_installer/start_myofinder.bat
@@ -41,7 +41,7 @@ echo Checking if the dependencies are installed
     echo The dependencies are installed
 ) || (
     echo The dependencies are not installed, installing them
-    %base_path%\venv\Scripts\python -m pip install myofinder==1.0.4
+    %base_path%\venv\Scripts\python -m pip install myofinder==1.0.5
 )
 
 echo.

From 7f0f4750862edfa18822e58cbcea7c86a113fddf Mon Sep 17 00:00:00 2001
From: Antoine Weisrock <antoine.weisrock@gmail.com>
Date: Mon, 2 Oct 2023 10:41:13 +0200
Subject: [PATCH 3/4] docs: improve style of description on PyPI

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index eaabd06..465b785 100644
--- a/setup.py
+++ b/setup.py
@@ -27,7 +27,7 @@
   of them, visualizing the output, and manually correcting it if needed. It 
   relies on the DeepCell library for performing the image segmentation.
   """,
-  long_description_content_type='text/plain',
+  long_description_content_type='text/x-rst',
   keywords='segmentation,fusion index,automation,muscle culture',
   license='GPL V3',
   classifiers=['Development Status :: 5 - Production/Stable ',

From d5ee3e106de9ba0d7d685808e96202673689ed0b Mon Sep 17 00:00:00 2001
From: WeisLeDocto <antoine.weisrock@gmail.com>
Date: Mon, 2 Oct 2023 10:43:22 +0200
Subject: [PATCH 4/4] build: update Windows installer after version update to
 1.0.5

---
 bin/myofinder.msi | Bin 2477568 -> 2477568 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/bin/myofinder.msi b/bin/myofinder.msi
index 3931151e5f1371cb882a850e4df6220295143db4..59454fbdc5f16a14eca80ccd1ab7692e7e933076 100644
GIT binary patch
delta 798
zcmZpeGo7&kh&SZ0uqjwxP3QUAT*T5|#KH)~OhC*G#2`K^5VHX>I}mdKF((jn0Wmia
z^8hg~5c2^sKM)H5u^<o&0kJR;ivY1G5Q_n^I1oz!u_O>n0kJd?%K)(~5X%9vJP<1Y
zu_6#F0kJX=t86b~QGJ-rXu3V5Kvh&i+|A6$(AnI~Sl86W*+|#K!rWBX$<4)Wdqan6
zqau&Fp`p2ng`tzHg|X>&-c_pi<)I#%{^_KuOTAOLN2mfraY<rPNqlZ)ep+T;N@|f_
zQep|igUKuB{$=E1bM~GZl9+wlK;UoQhx#3Clh$5HJG~&DOH*3A^$=UL$hV^gAwOlZ
zr>ZKRJjwI(qxH?+*T?)G|GF&s`tIKEfBddrFHl!;TBd7pevNn*uf29{`TD$zO#ufI
zl-KCbWC^Jc$qZfa>EYr0g+Y5u3q{=HCq9=dnbs=aE~nOi=Ar!IntgMo@vYrxwb=0T
zli7yb&uo6u{>(@1?E+7RYrgxQpP0|YIq~57Q_rIs3rzY>cy?-D*nM7bhn~;Ni^nEr
z^2NsGU9fVz+N-5nvva0yf?0EaA<LI5Yu&e6x8Kd<*qX{W<y(D9$jT}Mi`NYAW<OJS
zv0=kGX5|Lm(Bom-(ws~M4xgBx{>8qjrmBT?<Bi{j@+N9$)V%*I@wcRS>2kiY`OEVw
zYPvyg{lPC&=e0k+QS9*Y!<CmI$;qy~yBYE(Ufn3Tk5SBj<%YXI7k}Ydc7}0jW<<!Q
zg_CX9x$iRYRJpwBWtqz}f%-2?uGRkHTJcimlk`#>*Jdr(qpZBiV)2h8-P?I5i*7$u
zF?|n@*`WrWXKys}wMy?DTC$>KMdrr7^@k64Ufk;|!NO7;b>Zkfo>v}G7Z<p9RUC8j
zuG<-N#{T^JduA7(pD7R1exrH)T2MmjS3Px0AD6@}UoRBCKd@P_xN6(ll14jzrI784
xLD8qKNnN_MZ&#-Mmgz!IyKl_d`?)OQ>$`V>H#4UmyEwfuRndO?0WIcSMgYsqS;+tZ

delta 794
zcmZpeGo7&kh&SZ0uzd)h)wSzWa}i5>5ep*_GXXI(5QF%vK+Fcj>_E%`#GF9P1;pGy
z%mc){K+Ffk{6H)K#DYL91jNEXECR%$Kr9Bt;y^3`#F9WP1;o-oECa-{Kr9Eu@<6Nr
z#EL+y1jNcftg^j`MfG7eqsjJ=0##87aT6m`3kydV16?;`BLiI%S4U%A3nv4!?F}8O
zjfy;$&IZm-ZUz>v2F?cCc~`04mxp?6`lpksF7>wI;c*HK#U+VFCGokH`DvMXDXB$z
zNr@#4k9<GP`^(71=IlK+Br*H8fxzFq5A{3PCat}YcKXF~r&Gtg7H&AG&{}KA6KZ!n
zD%I1Y$jG_wk6+p2T^ld&_*ZhQs{Fm}{>xuY?{Icb$mBj}{JJ&j@OiKMcUMPmQ4le>
z!SUK#jZw5dG)i<u&5sY!D?;*PWsY79f3lNpZtBCM3)@dB7ymeJFkgT9Qs?Y7=Q7Ti
z{7gHe`&sAbLd(gX))_(#rIX)Vep>F}l=5Nqr=4L6GQG-0K}lR+-W9W~;|{LcQkXK!
zdHQteEq(!|i@iAG^U}CyoPCfi!)ROjI`Hke#O=~fxiguU+SW^ku9D+9XVvg~nI(sn
z&YI5$I1;?CZk)PyW&rOIgHO*T|Mn})mrHci`Bry^y_a+I$xHiBFe}as@@BI3w{PBe
zP1Waiyg}{K=MOEu$pl#0lv-WA5fOM;uOT|6G^ZuM;b^c{PWe9#+h)yThfFE4sW~rF
z`d?4f^AS3^C2N=LL`#->+m)sB_c3Kzwf}L`^uM^kE3nY<@QkC=D~?@EJe+cLt-(E2
z{pMZ+g=S0ZQ?tG1Za2`>lFf=*^Z50Lf~1msVK&BtbHqwE>Ni_W3Nv{zQEA@B3zOpY
z#6O?^yn4Iu7t7CcuX0tN+PYOFB69C(Pd?#5iCo)~JJug^j?9^ts~x-GJhSrE+>R^L
rHf?R&vSoeVE&jJlU4AN=rN7@J8@6|Mbx2v%(!wwD+c#=4uVw@Q;qg!E