# HG changeset patch
# User bgruening
# Date 1750595134 0
# Node ID 8b9500115e699f93b873e9adeef666f5ac340bd0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
diff -r 000000000000 -r 8b9500115e69 macros.xml
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+++ b/macros.xml Sun Jun 22 12:25:34 2025 +0000
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+ 1.3.0
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+ quay.io/bgruening/vpt:1.3.0-1
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+ advanced_output['log']
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+ @Manual{github,
+ title = {Vizgen Post-processing Tool},
+ author = {Vizgen},
+ organization = {Vizgen},
+ year = {2022},
+ url = {https://github.com/Vizgen/vizgen-postprocessing}}
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diff -r 000000000000 -r 8b9500115e69 vpt_segment.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/vpt_segment.xml Sun Jun 22 12:25:34 2025 +0000
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+ cells and refine MERSCOPE experiments
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+ macros.xml
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+ [0-9a-zA-Z_]+
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+The Vizgen Post-processing Tool (VPT) is a scalable and reproducible tool which enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
+
+The **Vizgen Post-processing Tool - Segment Cells** performes **run_segmentation**, **partition_transcripts**, **sum_signals**, **derive-entity-metadata**, and **generate-segmentation-metrics** of the VPT pipeline. The segmentation
+
+Segmentation parameters for CellPose can be assigned with "**Segmentation configuration file**".
+
+The segmentation parameters describes a series of steps to perform on the input data. Using the same segmentation algorithm on a series of experiments ensures that they are processed identically and reproducibly.
+
+The segmentation parameters has 3 main sections:
+
+1. **Experiment properties**:
+ - Holds descriptions of the way the data was collected. Specifically, it must contain a list of the z-indexes and z-positions in the data. This data is used to apply 2D segmentation to 3D data and calculate distances on the z-axis.
+2. **Segmentation tasks**:
+ - Holds a list of segmentation tasks to perform. These tasks will be performed sequentially. By running different segmentation tools in "tasks" and combining their output, it is possible to improve cell detection. For example, combining the results of CellPose with the `cyto2` model and the `nuclei` model can dramatically improve the segmentation F1 score over either method alone.
+3. **Segmentation task fusion**:
+ - Specifies how the geometries produced by each segmentation task should be combined. All `segmentation_task_fusion` options will produce a non-overlapping set of valid geometries.
+4. **Output files**:
+ - Specifies which entity types should be written to disk in the output folder and the file names they should receive.
+
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+For more information on the VPT pipeline, please refer to the `VPT user guide`_
+
+-----
+
+If you want to use a custom-trained model, set the CellPose model to null and provide the custom weights file.
+
+
+.. class:: infomark
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+**Note:** VPT only supports **9** tasks in a single segmentation algorithm. If more tasks are needed, users are encouraged to run vpt multiple times and combine the segmentation outputs post hoc.
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+.. class:: infomark
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+**Note:** VPT tool on Galaxy only uses **CellPose** algorithm for cell segmentation.
+
+.. _`VPT user guide`: https://vizgen.github.io/vizgen-postprocessing/
+
+
+
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