Micro-Manager support

POLCAM-SR/POLCAM-SR.prj

@@ -1,5 +1,5 @@
 <deployment-project plugin="plugin.apptool" plugin-version="1.0">
-  <configuration build-checksum="4047185125" file="/Users/ezrabruggeman/Documents/GitHub/POLCAM-SR/POLCAM-SR/POLCAM-SR.prj" location="/Users/ezrabruggeman/Documents/GitHub/POLCAM-SR/POLCAM-SR" name="POLCAM-SR" target="target.mlapps" target-name="Package App">
+  <configuration build-checksum="593887742" file="/Users/ezrabruggeman/Documents/GitHub/POLCAM-SR/POLCAM-SR/POLCAM-SR.prj" location="/Users/ezrabruggeman/Documents/GitHub/POLCAM-SR/POLCAM-SR" name="POLCAM-SR" target="target.mlapps" target-name="Package App">
     <param.appname>POLCAM-SR</param.appname>
     <param.authnamewatermark>Ezra Bruggeman</param.authnamewatermark>
     <param.email>eb758@cam.ac.uk</param.email>
@@ -11,9 +11,9 @@
       <file>${PROJECT_ROOT}/POLCAM-SR_resources/icon_16.png</file>
     </param.icons>
     <param.summary>Application to process single-molecule and diffraction-limited polarisation camera image data</param.summary>
-    <param.description />
-    <param.screenshot>/private/var/folders/6j/9pmd1ms95nn1t7d0_vmbff240000gn/T/tpf8aa7ce1_c2fb_44b5_a603_61d43a037f70.png</param.screenshot>
-    <param.version>1.2</param.version>
+    <param.description>Process single-molecule and diffraction-limited polarisation camera data</param.description>
+    <param.screenshot>/private/var/folders/6j/9pmd1ms95nn1t7d0_vmbff240000gn/T/tp5fcb071b_fce0_4f70_936f_97e7dfa348c7.png</param.screenshot>
+    <param.version>1.1.1</param.version>
     <param.products.name />
     <param.products.id />
     <param.products.version />
@@ -24,7 +24,6 @@
       <param.authnamewatermark />
       <param.email />
       <param.company />
-      <param.description />
       <param.products.name />
       <param.products.id />
       <param.products.version />
@@ -56,7 +55,8 @@
       <file>${PROJECT_ROOT}/lib/+Utils/getAverageIntensityProjectionFromPath.m</file>
       <file>${PROJECT_ROOT}/lib/+Utils/getMaximumIntensityProjectionFromPath.m</file>
       <file>${PROJECT_ROOT}/lib/+Utils/getMinimumIntensityProjectionFromPath.m</file>
-      <file>${PROJECT_ROOT}/lib/+Utils/getOrderedImageFilelist.m</file>
+      <file>${PROJECT_ROOT}/lib/+Utils/getOrderedImageFilelist_MicroManager.m</file>
+      <file>${PROJECT_ROOT}/lib/+Utils/getOrderedImageFilelist_ThorCam.m</file>
       <file>${PROJECT_ROOT}/lib/+Utils/getSumIntensityProjectionFromPath.m</file>
       <file>${PROJECT_ROOT}/lib/+Utils/readJsonFile.m</file>
       <file>${PROJECT_ROOT}/lib/+Utils/readTiffStack.m</file>

POLCAM-SR/docs/default settings/lastVisitedDirectories.json

@@ -1,4 +1,4 @@
 {
-  "pathLastImg": "/Users/ezrabruggeman/Documents/GitHub/POLCAM-SR/POLCAM-SR/docs/samples/fibrils/",
+  "pathLastImg": "/Users/ezrabruggeman/Desktop/test TC",
   "pathLastLocs": "/Users/ezrabruggeman/Documents/GitHub/POLCAM-SR/POLCAM-SR/docs/samples/fibrils/"
 }

POLCAM-SR/lib/+Utils/getOrderedImageFilelist_MicroManager.m

@@ -0,0 +1,35 @@
+function filelist = getOrderedImageFilelist_MicroManager(directory)
+
+% get list of all files with tif extension
+filelist_tif = dir(fullfile(directory,'*_MMStack_Default.ome.tif'));
+
+% remove files that start with '.' (sometimes there are hidden files on mac)
+filelist_tif = filelist_tif(~startsWith({filelist_tif.name},'.'));
+
+if isempty(filelist_tif)
+    filelist = 0;
+else
+    % sort files in ascending order
+    filelist_tif = struct2table(filelist_tif);
+    filelist_tif = sortrows(filelist_tif,'name','ascend');
+
+    % format for POLCAM-SR
+    filelist = struct;
+    for i=1:height(filelist_tif)
+        [~,baseName_img,~] = fileparts(filelist_tif.name(i));
+        filelist(i).filepath = char(fullfile(directory,filelist_tif.name(i)));
+        filelist(i).baseName = extractBefore(baseName_img,'_MMStack_Default.ome');
+
+        % find position of underscores '_' in filename
+        indeces_underscore = strfind(filelist(i).baseName,'_');
+        % get the index of the last underscore
+        index_last_underscore = indeces_underscore(end);
+        % extract the number after the last underscore
+        filelist(i).id = str2double(filelist(i).baseName(index_last_underscore+1:end));
+    end
+    % sort filenames based on suffix to get correct frame numbers
+    [~,idx] = sort([filelist.id]);
+    filelist = filelist(idx);
+end
+
+end

POLCAM-SR/lib/+Utils/getOrderedImageFilelist_ThorCam.m

@@ -0,0 +1,29 @@
+function filelist = getOrderedImageFilelist_ThorCam(directory)
+
+% get list of all files with tif extension
+filelist_tif = dir(fullfile(directory,'*.tif'));
+
+% remove files that start with '.' (sometimes there are hidden files on mac)
+filelist_tif = filelist_tif(~startsWith({filelist_tif.name},'.'));
+
+if isempty(filelist_tif)
+    filelist = 0;
+else
+    filelist = struct;
+    for i=1:length(filelist_tif)
+        [~,baseName_img,~] = fileparts(filelist_tif(i).name);
+        filelist(i).filepath = fullfile(directory,filelist_tif(i).name);
+        filelist(i).baseName = baseName_img;
+
+        % find position of underscores '_' in filename
+        indeces_underscore = strfind(filelist(i).baseName,'_');
+        % get the index of the last underscore
+        index_last_underscore = indeces_underscore(end);
+        filelist(i).id = str2double(filelist(i).baseName(index_last_underscore+1:end));
+    end
+    % sort filenames based on suffix to get correct frame numbers
+    [~,idx] = sort([filelist.id]);
+    filelist = filelist(idx);
+end
+
+end

POLCAM-SR/lib/dev/test_uManager_ordered_filelist.m

@@ -0,0 +1,45 @@
+
+close all
+clear all
+clc
+
+directory = '/Users/ezrabruggeman/Desktop/test MM';
+
+
+%%
+
+% get list of all files with tif extension
+filelist_tif = dir(fullfile(directory,'*_MMStack_Default.ome.tif'));
+
+% remove files that start with '.' (sometimes there are hidden files on mac)
+filelist_tif = filelist_tif(~startsWith({filelist_tif.name},'.'));
+
+if isempty(filelist_tif)
+    filelist = 0;
+else
+    % sort files in ascending order
+    filelist_tif = struct2table(filelist_tif);
+    filelist_tif = sortrows(filelist_tif,'name','ascend');
+
+    % format for POLCAM-SR
+    filelist = struct;
+    for i=1:height(filelist_tif)
+        [~,baseName_img,~] = fileparts(filelist_tif.name(i));
+        filelist(i).filepath = char(fullfile(directory,filelist_tif.name(i)));
+        filelist(i).baseName = extractBefore(baseName_img,'_MMStack_Default.ome');
+    end
+
+    % sort filenames based on suffix to get correct frame numbers (ASSUMES THORCAM INDEXING)
+    for i=1:length(filelist)
+        % find position of underscores '_' in filename
+        indeces_underscore = strfind(filelist(i).baseName,'_');
+        % get the index of the last underscore
+        index_last_underscore = indeces_underscore(end);
+        % extract the number after the last underscore
+        filelist(i).id = str2double(filelist(i).baseName(index_last_underscore+1:end));
+    end
+    [~,idx] = sort([filelist.id]);
+    filelist = filelist(idx);
+end
+
+

README.md

@@ -2,6 +2,7 @@
 
 Software for processing single-molecule and diffraction limited polarisation camera image data.
 
+The POLCAM-SR software is described in our [bioRxiv preprint](https://doi.org/10.1101/2023.02.07.527479). Documentation can be found on the [POLCAM website](https://theleelab.github.io/POLCAM-site/software_polcam_sr).
 
 ## Requirements
 
@@ -21,3 +22,13 @@ You can install `POLCAM-SR` as a MATLAB plugin. [Click here](https://github.com/
 ## Issues
 
 If you encounter any problems, please [file an issue](https://github.com/ezrabru/POLCAM-SR/issues) along with a detailed description.
+Please also do not hesitate to contact us at eb758@cam.ac.uk with any questions about the installation and/or use of the software.
+
+## Citing POLCAM-SR
+
+If you use POLCAM-SR in your research, please cite our preprint describing the software.
+
+E. Bruggeman, O. Zhang, L-M. Needham, M. Körbel, S. Daly, M. Cheetham, R. Peters, T. Wu, A.S. Klymchenko, S.J. Davis , E.K. Paluch , D. Klenerman , M.D. Lew , K. O’Holleran and S.F. Lee <br> 
+POLCAM: Instant molecular orientation microscopy for the life sciences <br>
+bioRxiv (2023). https://doi.org/10.1101/2023.02.07.527479
+