Modified pretrained_models.yaml to contain model catalog information with description, primary site, and supported sites. - #1106
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mraoaakash wants to merge 10 commits into
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Modified pretrained_models.yaml to contain model catalog information with description, primary site, and supported sites.#1106mraoaakash wants to merge 10 commits into
pretrained_models.yaml to contain model catalog information with description, primary site, and supported sites.#1106mraoaakash wants to merge 10 commits into
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mraoaakash
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pretrained_models.yaml to contain model catalog information with description, primary site, and supported sites.
for more information, see https://pre-commit.ci
…atoolbox into pretrainedmodels
for more information, see https://pre-commit.ci
shaneahmed
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Aug 7, 2026
| @@ -1,5 +1,11 @@ | |||
| alexnet-kather100k: | |||
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Add class dictionary for the output for each channel from raw output in all cases.
shaneahmed
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Aug 7, 2026
| @@ -1,5 +1,11 @@ | |||
| alexnet-kather100k: | |||
| hf_repo_id: TIACentre/TIAToolbox_pretrained_weights | |||
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@gozdeg Please can you add information from https://github.com/TissueImageAnalytics/tiatoolbox-qupath-extension/blob/8d6e65085d84beb1f4e2f21adaeecc45f7447890/src/main/resources/qupath/ext/tiatoolbox/ui/models.json in this file.
shaneahmed
reviewed
Aug 7, 2026
| @@ -1,5 +1,11 @@ | |||
| alexnet-kather100k: | |||
| hf_repo_id: TIACentre/TIAToolbox_pretrained_weights | |||
| catalog: | |||
shaneahmed
reviewed
Aug 7, 2026
| num_output_channels: 5 | ||
| encoder: "resnet50" | ||
| decoder_block: [3, 3] | ||
| class_dict: {0: "Tumour", 1: "Stroma", 2: "Inflamatory", 3: "Necrosis", 4: "Others"} |
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We do not need to remove class_dict. Instead we should add these for the missing ones.
shaneahmed
reviewed
Aug 7, 2026
| @@ -0,0 +1,3 @@ | |||
| version = 1 | |||
shaneahmed
reviewed
Aug 7, 2026
| hf_repo_id: TIACentre/TIAToolbox_pretrained_weights | ||
| catalog: | ||
| description: > | ||
| Predict Normal, Debri, Tumor, Adipose, Mucus, Smooth, Stroma, Lymphocytes regions at a patch level in colon images. |
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Suggested change
| Predict Normal, Debri, Tumor, Adipose, Mucus, Smooth, Stroma, Lymphocytes regions at a patch level in colon images. | |
| Predict Normal, Debris, Tumor, Adipose, Mucus, Smooth, Stroma, Lymphocytes regions at a patch level in colon images. |
shaneahmed
reviewed
Aug 7, 2026
| hf_repo_id: TIACentre/TIAToolbox_pretrained_weights | ||
| catalog: | ||
| description: > | ||
| Predict Normal, Debri, Tumor, Adipose, Mucus, Smooth, Stroma, Lymphocytes regions at a patch level in colon images. |
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Suggested change
| Predict Normal, Debri, Tumor, Adipose, Mucus, Smooth, Stroma, Lymphocytes regions at a patch level in colon images. | |
| Predict Normal, Debris, Tumor, Adipose, Mucus, Smooth, Stroma, Lymphocytes regions at a patch level in colon images. |
shaneahmed
reviewed
Aug 7, 2026
| description: > | ||
| Predict Normal, Debri, Tumor, Adipose, Mucus, Smooth, Stroma, Lymphocytes regions at a patch level in colon images. | ||
| primary_site: colon | ||
| supported_sites: |
shaneahmed
reviewed
Aug 7, 2026
| catalog: | ||
| description: > | ||
| Predict Normal, Debri, Tumor, Adipose, Mucus, Smooth, Stroma, Lymphocytes regions at a patch level in colon images. | ||
| primary_site: colon |
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Suggested change
| primary_site: colon | |
| tissue_types: colon |
shaneahmed
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Aug 7, 2026
| @@ -1,5 +1,11 @@ | |||
| alexnet-kather100k: | |||
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At the top of the file, explain in comments what different fields mean in this file.
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Partial PR for addition of pre-trained model documentation to the pretrained_model.yaml file. Includes the addition of a new filed called
catalogto each model yaml entry. The entry is structured in the following manner:catalog: description: > multi-line model description primary_site: primary site that model is supported for (agnostic for site-agnostic or multi-site models) supported_sites: - other - supported - sitesFields can be read nested and used for downstream filtering tasks as necessary.
NOTE: This is a partial PR and does not contain the complete set of catalog entries as it proved difficult to ascertain the required catalog entries for some models. Someone with more complete knowledge of some models would have to take up the completion of the remaining catalog entries.
Description, primary site, and supported sites:
Description only: