diff --git a/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/CHANGELOG.md b/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/CHANGELOG.md index 2169bdc88..9e7ee47ad 100644 --- a/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/CHANGELOG.md +++ b/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.2] - 2024-11-07 + +- Upgrade the tests of the workflow +- Upgrade the segmentation-and-counting.ga workflow to recent tool versions + ## [0.1] - 2024-02-29 -- Creation of workflow for segmentation and counting of cell nuclei in fluorescence microscopy images. +- Creation of workflow for segmentation and counting of cell nuclei in fluorescence microscopy images. \ No newline at end of file diff --git a/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/segmentation-and-counting-tests.yml b/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/segmentation-and-counting-tests.yml index 35facddc5..32f565b55 100644 --- a/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/segmentation-and-counting-tests.yml +++ b/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/segmentation-and-counting-tests.yml @@ -7,13 +7,12 @@ outputs: overlay_image: path: test-data/overlay_image.png - compare: sim_size - delta: 100 + compare: image_diff objects_count: path: test-data/objects_count.tabular compare: diff lines_diff: 0 label_image: path: test-data/label_image.tiff - compare: sim_size - delta: 100 + compare: image_diff + metric: iou diff --git a/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/segmentation-and-counting.ga b/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/segmentation-and-counting.ga index 962daf4de..2fb279652 100644 --- a/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/segmentation-and-counting.ga +++ b/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/segmentation-and-counting.ga @@ -11,7 +11,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1", + "release": "0.2", "name": "Segmentation and counting of cell nuclei in fluorescence microscopy images", "steps": { "0": { @@ -37,13 +37,13 @@ "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "5dd476ec-c0d7-45af-a522-ba6b2ce43880", + "uuid": "facec436-5d6e-43de-a21e-cebc8272a35c", "when": null, "workflow_outputs": [] }, "1": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3-3", + "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/1.12.0+galaxy1", "errors": null, "id": 1, "input_connections": { @@ -54,7 +54,7 @@ }, "inputs": [], "label": null, - "name": "Filter 2D image", + "name": "Filter 2-D image", "outputs": [ { "name": "output", @@ -66,23 +66,23 @@ "top": 244.80388558482915 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3-3", + "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/1.12.0+galaxy1", "tool_shed_repository": { - "changeset_revision": "f70b215d155c", + "changeset_revision": "d51310ab328a", "name": "2d_simple_filter", "owner": "imgteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - 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"tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.0.1-2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.18.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "77f7159d775a", + "changeset_revision": "b1c2c210813c", "name": "2d_histogram_equalization", "owner": "imgteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"tiff\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"h_type\": \"clahe\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.0.1-2", + "tool_version": "0.18.1+galaxy0", "type": "tool", - "uuid": "06f11435-5172-4a40-8002-762d3d60ae46", + "uuid": "c4b63332-c0ed-4a40-9670-9d5ba2a5e88f", "when": null, "workflow_outputs": [] }, "3": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5-2", + "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy3", "errors": null, "id": 3, "input_connections": { @@ -144,23 +144,23 @@ "top": 243.376959571321 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5-2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy3", "tool_shed_repository": { - "changeset_revision": "3df9f0a4bf34", + "changeset_revision": "699a5e9146b3", "name": "2d_auto_threshold", "owner": "imgteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__input_ext\": \"input\", \"block_size\": \"5\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dark_bg\": true, \"input\": {\"__class__\": \"ConnectedValue\"}, \"th_method\": \"otsu\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.0.5-2", + "tool_state": "{\"__input_ext\": \"input\", \"block_size\": \"5\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dark_bg\": \"true\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert_output\": false, \"th_method\": {\"method_id\": \"otsu\", \"__current_case__\": 1, \"threshold\": \"0\", \"block_size\": \"0\", \"offset\": \"0.0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.18.1+galaxy3", "type": "tool", - "uuid": "88c61ddf-7751-41e3-b4a1-f0829969b5b2", + "uuid": "d75a2027-d855-4f05-9261-25f2f712efce", "when": null, "workflow_outputs": [] }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy3", "errors": null, "id": 4, "input_connections": { @@ -183,17 +183,17 @@ "top": 0 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy3", "tool_shed_repository": { - "changeset_revision": "85edbb7a436b", + "changeset_revision": "fcadded98e61", "name": "bfconvert", "owner": "imgteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"tiff\", \"bigtiff\": false, \"channel_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"compression\": \"False\", \"crop_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"noflat\": true, \"out_format\": \"png\", \"pyramid_options\": {\"generate\": \"False\", \"__current_case__\": 1}, \"range_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"series_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"tile_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"timepoint_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"z_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "6.7.0+galaxy2", + "tool_version": "6.7.0+galaxy3", "type": "tool", - "uuid": "8cc184c2-5e9d-42b2-9af1-3ba71030eda4", + "uuid": "a6a689c6-c1d0-4929-87a2-ac5206cf8026", "when": null, "workflow_outputs": [] }, @@ -232,19 +232,19 @@ "tool_state": "{\"__input_ext\": \"tiff\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"mode_selector\": \"cca\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.5+galaxy0", "type": "tool", - "uuid": "8e9ab2d1-f119-4cbd-8afc-175a2b99a1b9", + "uuid": "cd899592-8b30-4a79-9aba-f75a10c75dd7", "when": null, "workflow_outputs": [ { "label": "label_image", "output_name": "output", - "uuid": "8296aad6-d5d9-427c-8a83-662b7ea47358" + "uuid": "daaee143-81e0-4067-aac0-81f02732c343" } ] }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.4+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.4+galaxy4", "errors": null, "id": 6, "input_connections": { @@ -257,7 +257,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Overlay images", + "name": "method_option" + }, + { + "description": "runtime parameter for tool Overlay images", + "name": "method_option" + } + ], "label": null, "name": "Overlay images", "outputs": [ @@ -271,23 +280,23 @@ "top": 104.58436042741572 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.4+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.4+galaxy4", "tool_shed_repository": { - "changeset_revision": "37662cbf44b8", + "changeset_revision": "ca362a9bfa20", "name": "overlay_images", "owner": "imgteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"method_option\": {\"method\": \"seg_contour\", \"__current_case__\": 2, \"im1\": {\"__class__\": \"ConnectedValue\"}, \"im2\": {\"__class__\": \"ConnectedValue\"}, \"thickness\": \"2\", \"color\": \"#ff0000\", \"show_label\": true, \"label_color\": \"#ffff00\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.0.4+galaxy0", + "tool_version": "0.0.4+galaxy4", "type": "tool", - "uuid": "1f96ef1a-d94c-4a95-9148-106789d12355", + "uuid": "066a4e0d-2ae3-46f7-a0c8-77a1a83d119a", "when": null, "workflow_outputs": [ { "label": "overlay_image", "output_name": "out_png", - "uuid": "dd94858e-ce8c-4f89-9e31-5e4666887f2b" + "uuid": "5b94aaa3-9034-465e-995f-3d8f1f057f4b" } ] }, @@ -326,13 +335,13 @@ "tool_state": "{\"__input_ext\": \"tiff\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.0.5-2", "type": "tool", - "uuid": "9bda49f1-24ec-42f8-bceb-ab54c56b6624", + "uuid": "75a4d4d8-0435-441f-a309-d04071cf125f", "when": null, "workflow_outputs": [ { "label": "objects_count", "output_name": "output", - "uuid": "fd812c33-336d-4958-9877-b5b5b337f1d1" + "uuid": "8b3d51a7-2c1f-4f84-ac80-ef0ef6d25a3f" } ] } diff --git a/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/test-data/label_image.tiff b/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/test-data/label_image.tiff index bce30bc66..3f357e031 100644 Binary files a/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/test-data/label_image.tiff and b/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/test-data/label_image.tiff differ diff --git a/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/test-data/overlay_image.png b/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/test-data/overlay_image.png index 1d8d5b327..473a2993b 100644 Binary files a/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/test-data/overlay_image.png and b/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/test-data/overlay_image.png differ