From e6495c053c6b5cce499902c1ef85113c15bc5939 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Thu, 19 Dec 2024 12:57:48 +0100 Subject: [PATCH 01/10] remove 'other' --- bioimageio/spec/static/tag_categories.json | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/bioimageio/spec/static/tag_categories.json b/bioimageio/spec/static/tag_categories.json index a84ea805b..bdb19f622 100644 --- a/bioimageio/spec/static/tag_categories.json +++ b/bioimageio/spec/static/tag_categories.json @@ -9,8 +9,7 @@ "x-ray-microscopy", "force-microscopy", "high-content-imaging", - "whole-slide-imaging", - "other" + "whole-slide-imaging" ], "dims": [ "2d", @@ -61,4 +60,4 @@ "in-silico-labeling" ] } -} \ No newline at end of file +} From 52673ff03400ac0e71c8c4fe3e3222f59052c5aa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Thu, 19 Dec 2024 15:43:58 +0100 Subject: [PATCH 02/10] reduntant with given weights --- bioimageio/spec/static/tag_categories.json | 5 ----- 1 file changed, 5 deletions(-) diff --git a/bioimageio/spec/static/tag_categories.json b/bioimageio/spec/static/tag_categories.json index bdb19f622..c2ba28837 100644 --- a/bioimageio/spec/static/tag_categories.json +++ b/bioimageio/spec/static/tag_categories.json @@ -29,11 +29,6 @@ "brain", "whole-organism" ], - "framework": [ - "tensorflow", - "pytorch", - "tensorflow.js" - ], "software": [ "ilastik", "imagej", From 5af5b78dd79e8c50bef3761c2632b5545ba37b65 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Thu, 19 Dec 2024 15:44:59 +0100 Subject: [PATCH 03/10] redundant to compatibiliy checks --- bioimageio/spec/static/tag_categories.json | 8 -------- 1 file changed, 8 deletions(-) diff --git a/bioimageio/spec/static/tag_categories.json b/bioimageio/spec/static/tag_categories.json index c2ba28837..2c3a20521 100644 --- a/bioimageio/spec/static/tag_categories.json +++ b/bioimageio/spec/static/tag_categories.json @@ -29,14 +29,6 @@ "brain", "whole-organism" ], - "software": [ - "ilastik", - "imagej", - "fiji", - "imjoy", - "deepimagej", - "n2v" - ], "network": [ "unet", "densenet", From b3ff5ce63c6c2e14527bfeff5424a115e83c9f01 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Thu, 19 Dec 2024 15:47:58 +0100 Subject: [PATCH 04/10] not really relevant --- bioimageio/spec/static/tag_categories.json | 7 ------- 1 file changed, 7 deletions(-) diff --git a/bioimageio/spec/static/tag_categories.json b/bioimageio/spec/static/tag_categories.json index 2c3a20521..cb6bc2ac6 100644 --- a/bioimageio/spec/static/tag_categories.json +++ b/bioimageio/spec/static/tag_categories.json @@ -29,13 +29,6 @@ "brain", "whole-organism" ], - "network": [ - "unet", - "densenet", - "resnet", - "inception", - "shufflenet" - ], "task": [ "semantic-segmentation", "instance-segmentation", From 4aa7522f86cb39bfedb604813a82c56da1af023f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Thu, 19 Dec 2024 16:01:05 +0100 Subject: [PATCH 05/10] add light-microscopy --- bioimageio/spec/static/tag_categories.json | 1 + 1 file changed, 1 insertion(+) diff --git a/bioimageio/spec/static/tag_categories.json b/bioimageio/spec/static/tag_categories.json index cb6bc2ac6..adc1fe98d 100644 --- a/bioimageio/spec/static/tag_categories.json +++ b/bioimageio/spec/static/tag_categories.json @@ -3,6 +3,7 @@ "modality": [ "electron-microscopy", "cryo-electron-microscopy", + "light-microscopy", "fluorescence-light-microscopy", "transmission-light-microscopy", "super-resolution-microscopy", From 3b55bc5c03e0a608d260a4bfb5e9fe9ae66af4d2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Thu, 19 Dec 2024 16:36:23 +0100 Subject: [PATCH 06/10] add super-resolution (as task) --- bioimageio/spec/static/tag_categories.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bioimageio/spec/static/tag_categories.json b/bioimageio/spec/static/tag_categories.json index adc1fe98d..55aa2edd2 100644 --- a/bioimageio/spec/static/tag_categories.json +++ b/bioimageio/spec/static/tag_categories.json @@ -38,7 +38,8 @@ "denoising", "image-restoration", "image-reconstruction", - "in-silico-labeling" + "in-silico-labeling", + "super-resolution" ] } } From 23aaf5ff07f60c734f94969104737eeed8f6c338 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Thu, 19 Dec 2024 16:44:58 +0100 Subject: [PATCH 07/10] Create tag_aliases.json --- bioimageio/spec/static/tag_aliases.json | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 bioimageio/spec/static/tag_aliases.json diff --git a/bioimageio/spec/static/tag_aliases.json b/bioimageio/spec/static/tag_aliases.json new file mode 100644 index 000000000..f529cc925 --- /dev/null +++ b/bioimageio/spec/static/tag_aliases.json @@ -0,0 +1,3 @@ +{ + "electron-microscopy": ["EM"] +} From ae4f27828e939acac92bd242d22a6c271b93ab7a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Thu, 19 Dec 2024 16:47:30 +0100 Subject: [PATCH 08/10] add light-field-microscopy --- bioimageio/spec/static/tag_categories.json | 1 + 1 file changed, 1 insertion(+) diff --git a/bioimageio/spec/static/tag_categories.json b/bioimageio/spec/static/tag_categories.json index 55aa2edd2..8459a9359 100644 --- a/bioimageio/spec/static/tag_categories.json +++ b/bioimageio/spec/static/tag_categories.json @@ -3,6 +3,7 @@ "modality": [ "electron-microscopy", "cryo-electron-microscopy", + "light-field-microscopy", "light-microscopy", "fluorescence-light-microscopy", "transmission-light-microscopy", From f65fb3c1709de6f1167d4f5847ef53139b719dbf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Thu, 19 Dec 2024 16:48:20 +0100 Subject: [PATCH 09/10] Update tag_aliases.json --- bioimageio/spec/static/tag_aliases.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bioimageio/spec/static/tag_aliases.json b/bioimageio/spec/static/tag_aliases.json index f529cc925..86ce21a91 100644 --- a/bioimageio/spec/static/tag_aliases.json +++ b/bioimageio/spec/static/tag_aliases.json @@ -1,3 +1,4 @@ { - "electron-microscopy": ["EM"] + "electron-microscopy": ["EM"], + "light-field-microscopy": ["LFM"] } From 9c77ae8bccb31e3e6804316fc563a0920c9dc3fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Thu, 19 Dec 2024 17:02:05 +0100 Subject: [PATCH 10/10] draft categories for dataset and notebook types --- bioimageio/spec/static/tag_categories.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/bioimageio/spec/static/tag_categories.json b/bioimageio/spec/static/tag_categories.json index 8459a9359..738e8aac8 100644 --- a/bioimageio/spec/static/tag_categories.json +++ b/bioimageio/spec/static/tag_categories.json @@ -42,5 +42,11 @@ "in-silico-labeling", "super-resolution" ] + }, + "dataset": { + "modality": [""] + }, + "notebook": { + "task": [""] } }