update documentation examples

docs/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 727bb9b1d78a33f916926cb28f3549a4
+config: 58447cc7763988a8e2886fa512125b6f
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/html/_sources/pages/tutorials.rst.txt

@@ -6,7 +6,7 @@ Parsing and Stitching Data from Opera Phenix
 ============================================
 
 First you need to export your data from Harmony and rename the path to eliminate any spaces in the name.
-Then you can run the following script to parses and stitch your data.
+Then you can run the following script to parse and stitch your data.
 
 .. code-block:: python
     :caption: example script for parsing and stitching phenix data
@@ -32,18 +32,19 @@ Then you can run the following script to parses and stitch your data.
     overlap = 0.1 #adjust in case your data was aquired with another overlap
 
     #define parameters to find correct slide in experiment folder
-    row = 1
-    well = 1
-    zstack_value = 1
-    timepoint = str(1)
+    overlap = 0.1 #adjust in case your data was aquired with another overlap
+    row = str(2).zfill(2) #specify the row of the well you want to stitch
+    well = str(4).zfill(2) #specifc the well number you wish to stitch
+    zstack_value = str(1).zfill(3) #specify the zstack you want to stitch. for multiple zstacks please make a loop and iterate through each of them.
+    timepoint = str(1).zfill(3) #specifz the timepoint you wish to stitch
 
     #define on which channel should be stitched
     stitching_channel = "Alexa647"
     output_filetype = [".tif", "ome.zarr"] #one of .tif, .ome.tif, .ome.zarr (can pass several if you want to generate all filetypes)
 
     #adjust cropping parameter
     crop = {'top':0, 'bottom':0, 'left':0, 'right':0}  #this does no cropping
-    #crop = {'top':72, 'bottom':52, 'left':48, 'right':58} #this is good default values for an entire PPS slide with cell culture samples imaged with the SPARCSpy protocol
+    #crop = {'top':72, 'bottom':52, 'left':48, 'right':58} #this is good default values for an entire PPS slides with cell culture samples imaged with the SPARCS protocol
 
     #create output directory if it does not exist
     if not os.path.exists(outdir):
@@ -52,15 +53,26 @@ Then you can run the following script to parses and stitch your data.
     #define pattern to recognize which slide should be stitched
     #remember to adjust the zstack value if you aquired zstacks and want to stitch a speciifc one in the parameters above 
 
-    pattern = "Timepoint"+str(timepoint.zfill(3) +"_Row"+ str(row).zfill(2) + "_" + "Well" + str(well).zfill(2) + "_{channel}_"+"zstack"+str(zstack_value).zfill(3)+"_r{row:03}_c{col:03}.tif")
+    #you can define different rescale ranges for each channel if you want to or alternatively use the same range for all channels
+
+    #same range for all channels
+    rescale_range = (1, 99)
+
+    #custom for each channel
+    rescale_range = {"Alexa647":(1, 98), "DAPI":(1, 99), "mCherry":(1, 99)}  #channels need to be named as is the case in the parsed folder
+
+    pattern = f"Timepoint{timepoint}_Row{row}_Well{well}_{{channel}}_zstack{zstack_value}_r{{row:03}}_c{{col:03}}.tif"
     generate_stitched(input_dir, 
                         slidename,
                         pattern,
                         outdir,
                         overlap,
                         crop = crop ,
                         stitching_channel = stitching_channel, 
-                        filetype = output_filetype)
+                        filetype = output_filetype, 
+                        plot_QC = True, 
+                        do_intensity_rescale = True,
+                        rescale_range = rescale_range)
 
 Generated output
 ------------------
@@ -73,6 +85,7 @@ The stitching script will generate the following files:
     ├── QC_edge_quality.pdf
     ├── QC_edge_scatter.pdf
     ├── stitching_test.XML
+    ├── stitching_test.ome.zarr 
     ├── stitching_test_Alexa488.tif
     ├── stitching_test_DAPI.tif
     ├── stitching_test_mCherry.tif
@@ -91,6 +104,8 @@ The stitching script will generate the following files:
      - Plots the alignment quality against each other
    * - `stitching_test.XML`
      - contains the required input for reading the stitched files into BIAS
+   * - `<slidename>.ome.zarr`
+     - stitched image containing all channels in the ome.zarr format, optimal for viewing in napari
    * - `<slidename>_<channel_name>.tif`
      - stitched image for the given channel
    * - `stitching_test_tile_positions.tsv`
@@ -102,5 +117,3 @@ Example Results
 
 .. image:: ../_static/stitched_channels.png
     :width: 100 %
-
-    

docs/html/_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -222,7 +222,7 @@ table.modindextable td {
 /* -- general body styles --------------------------------------------------- */
 
 div.body {
-    min-width: 360px;
+    min-width: 450px;
     max-width: 800px;
 }
 
@@ -237,8 +237,14 @@ a.headerlink {
     visibility: hidden;
 }
 
-a:visited {
-    color: #551A8B;
+a.brackets:before,
+span.brackets > a:before{
+    content: "[";
+}
+
+a.brackets:after,
+span.brackets > a:after {
+    content: "]";
 }
 
 h1:hover > a.headerlink,
@@ -329,16 +335,12 @@ p.sidebar-title {
     font-weight: bold;
 }
 
-nav.contents,
-aside.topic,
 div.admonition, div.topic, blockquote {
     clear: left;
 }
 
 /* -- topics ---------------------------------------------------------------- */
 
-nav.contents,
-aside.topic,
 div.topic {
     border: 1px solid #ccc;
     padding: 7px;
@@ -377,17 +379,13 @@ div.body p.centered {
 
 div.sidebar > :last-child,
 aside.sidebar > :last-child,
-nav.contents > :last-child,
-aside.topic > :last-child,
 div.topic > :last-child,
 div.admonition > :last-child {
     margin-bottom: 0;
 }
 
 div.sidebar::after,
 aside.sidebar::after,
-nav.contents::after,
-aside.topic::after,
 div.topic::after,
 div.admonition::after,
 blockquote::after {
@@ -430,6 +428,10 @@ table.docutils td, table.docutils th {
     border-bottom: 1px solid #aaa;
 }
 
+table.footnote td, table.footnote th {
+    border: 0 !important;
+}
+
 th {
     text-align: left;
     padding-right: 5px;
@@ -613,26 +615,19 @@ ul.simple p {
     margin-bottom: 0;
 }
 
-aside.footnote > span,
-div.citation > span {
+dl.footnote > dt,
+dl.citation > dt {
     float: left;
+    margin-right: 0.5em;
 }
-aside.footnote > span:last-of-type,
-div.citation > span:last-of-type {
-  padding-right: 0.5em;
-}
-aside.footnote > p {
-  margin-left: 2em;
-}
-div.citation > p {
-  margin-left: 4em;
-}
-aside.footnote > p:last-of-type,
-div.citation > p:last-of-type {
+
+dl.footnote > dd,
+dl.citation > dd {
     margin-bottom: 0em;
 }
-aside.footnote > p:last-of-type:after,
-div.citation > p:last-of-type:after {
+
+dl.footnote > dd:after,
+dl.citation > dd:after {
     content: "";
     clear: both;
 }
@@ -649,6 +644,10 @@ dl.field-list > dt {
     padding-right: 5px;
 }
 
+dl.field-list > dt:after {
+    content: ":";
+}
+
 dl.field-list > dd {
     padding-left: 0.5em;
     margin-top: 0em;
@@ -674,16 +673,6 @@ dd {
     margin-left: 30px;
 }
 
-.sig dd {
-    margin-top: 0px;
-    margin-bottom: 0px;
-}
-
-.sig dl {
-    margin-top: 0px;
-    margin-bottom: 0px;
-}
-
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -752,14 +741,6 @@ abbr, acronym {
     cursor: help;
 }
 
-.translated {
-    background-color: rgba(207, 255, 207, 0.2)
-}
-
-.untranslated {
-    background-color: rgba(255, 207, 207, 0.2)
-}
-
 /* -- code displays --------------------------------------------------------- */
 
 pre {