Updated Backsub and docs (#590)

Backsub version 0.5.1 -- more lightweight and now supports compression when writing the output TIFF. The default pipeline configuration applies zlib compression.

Author: kbestak

config/defaults.yml

@@ -20,6 +20,7 @@ options:
   ilastik: --num_channels 1
   mcquant: --masks cell*.tif *_cp_masks*.tif
   naivestates: -p png
+  backsub: --compression zlib
   imagej-rolling-ball: 100 -n=4 -j="-Xmx4g"
 modules:
   illumination:
@@ -49,11 +50,11 @@ modules:
     -
       name: backsub
       container: ghcr.io/schapirolabor/background_subtraction
-      version: v0.4.1
+      version: v0.5.1
       cmd: |-
-        python3 /background_subtraction/background_sub.py \
-          -r ${image} -m ${marker} \
-          -o ${image_id}_backsub.ome.tif -mo markers_bs.csv
+        backsub \
+          --input ${image} --markers ${marker} \
+          --output "${image_id}_backsub.ome.tif" --marker-output markers_bs.csv
     -
       name: imagej-rolling-ball
       container: yuanchen12/imagej-rolling-ball

docs/parameters/core.md

@@ -836,16 +836,16 @@ workflow:
 
 ### Outputs
 
-* A pyramidal, tiled `.ome.tif`. Nextflow will write the output file to `background/` within the project directory.
+* A pyramidal, tiled `.ome.tif`. Nextflow will write the output file to `background/` within the project directory. By default, the output is compressed.
 * A modified `markers.csv` to match the background subtracted image.
 
 ### Optional arguments
 
 | Parameter | Default | Description |
 | --- | --- | --- |
 | `--pixel-size` | `None` | The resolution of the image in microns-per-pixel. If not provided, it is read from metadata. If that is not possible, 1 is assigned. |
-| `--tile-size` | `1024` | Tile size used for pyramid image generation.|
-| `--chunk-size` | `5000` | Chunk size used for lazy loading and processing the image.|
+| `--tile-size` | `256` | Tile size used for pyramid image generation.|
+| `--compression` | `zlib` | The output pyramidal OME-TIFF will be compressed using the specified compression. Set to "none" for no compression. "lzw", "zlib", or "none" are accepted options. |
 
 [Back to Other Modules](./core.html#other-modules){: .btn .btn-purple} [Back to top](./core){: .btn .btn-outline} 
 

docs/parameters/other.md

@@ -374,7 +374,7 @@ Nextflow will write all outputs to the `cell-states/naivestates/` subdirectory w
 
 ### Usage
 By default, MCMICRO assumes background subtraction should not be performed. Add `background: true` to [module options]({{site.baseurl}}/parameters/workflow.html#background) to indicate it should be. By default, the `background-method` parameter is set to `backsub`. 
-If channels are removed using this module, and `segmentation-channel` is specified, it should be kept in mind that the index provided with `segmentation-channel` would refer to the index after channel removal.
+If channels are removed using this module, and `segmentation-channel` is specified, it should be kept in mind that the index provided with `segmentation-channel` would refer to the index after channel removal. Note that if the corrected outputs are compressed, and a segmentation method fails, `segmentation-recyze` should be used to get around the issue.
 
 * Example `params.yml`:
 
@@ -393,15 +393,15 @@ workflow:
 
 ### Outputs
 
-* A pyramidal, tiled `.ome.tif`. Nextflow will write the output file to `background/` within the project directory.
+* A pyramidal, tiled `.ome.tif`. Nextflow will write the output file to `background/` within the project directory. By default, the output is compressed.
 * A modified `markers.csv` to match the background subtracted image.
 
 ### Optional arguments
 
 | Parameter | Default | Description |
 | --- | --- | --- |
 | `--pixel-size` | `None` | The resolution of the image in microns-per-pixel. If not provided, it is read from metadata. If that is not possible, 1 is assigned. |
-| `--tile-size` | `1024` | Tile size used for pyramid image generation.|
-| `--chunk-size` | `5000` | Chunk size used for lazy loading and processing the image.|
+| `--tile-size` | `256` | Tile size used for pyramid image generation.|
+| `--compression` | `zlib` | The output pyramidal OME-TIFF will be compressed using the specified compression. Set to "none" for no compression. "lzw", "zlib", or "none" are accepted options. |
 
 [Back to Other Modules](./core.html#other-modules){: .btn .btn-purple} [Back to top](./core){: .btn .btn-outline}