I'm trying to visualize the dataset with the Volume Cartographer, but it requires .volpkg. The dataset isn't in this format. How can we solve this?
\nThanks!
", "messages": [ { "id": 3343587, "postDate": "2025-11-21T18:58:57.033Z", "content": "I'm trying to visualize the dataset with the Volume Cartographer, but it requires .volpkg. The dataset isn't in this format. How can we solve this?
\nThanks!
", "rawMarkdown": "I'm trying to visualize the dataset with the Volume Cartographer, but it requires .volpkg. The dataset isn't in this format. How can we solve this?\n\nThanks!", "votes": 1 }, { "id": 3344776, "postDate": "2025-11-22T23:46:26.433Z", "content": "Are you using VC3D from https://github.com/ScrollPrize/villa/tree/main/volume-cartographer ? We don't support the upstream Volume Cartographer anymore. You'll need to piece together a volpkg directory from some segments, volume data, and a json configuration. Directions to do this can be found on the segmentation tutorial on our website: https://scrollprize.org/segmentation
", "rawMarkdown": "Are you using VC3D from https://github.com/ScrollPrize/villa/tree/main/volume-cartographer ? We don't support the upstream Volume Cartographer anymore. You'll need to piece together a volpkg directory from some segments, volume data, and a json configuration. Directions to do this can be found on the segmentation tutorial on our website: https://scrollprize.org/segmentation", "replies": [ { "id": 3348266, "postDate": "2025-11-25T17:46:05.163Z", "content": "Thanks. I was trying to use the https://github.com/educelab/volume-cartographer. I will certainly take a look at the tutorial, thank you!
", "rawMarkdown": "Thanks. I was trying to use the https://github.com/educelab/volume-cartographer. I will certainly take a look at the tutorial, thank you!", "replies": [ { "id": 3348387, "postDate": "2025-11-25T19:50:02.540Z", "rawMarkdown": "", "isDeleted": true } ] }, { "id": 3348388, "postDate": "2025-11-25T19:51:18.990Z", "content": "I've tried to follow the tutorial. I've created the folder scroll1.volpkg, and created the folders normal_grids, paths, volumes and the file config.json. Inside of the config.json I have {\"materialthickness\":1.0,\"name\":\"Example\",\"version\":7}. Then, inside of the folder volumes I have two subfolders s1_uint8_ome and 050_entire_scroll1_ome. Each subfolder contains a .tif file 2290837.tif. In the first subfolder is the image and in the second is the segmentation, also in the .tif format. Then, inside of each folder I also have the meta.json file, with the content {\"height\":320,\"max\":65535.0,\"min\":0.0,\"name\":\"Example_raw\",\"slices\":320,\"type\":\"vol\",\"uuid\":\"20231117143551-s3_raw\",\"voxelsize\":1,\"width\":320, \"format\":\"tif\"}. The .volpkg is loaded correctly and the names appear correct, however, no image is shown. The planes are all white. Could you please assist me on this? Thank you!
OK, so what you're trying to do is not currently supported by VC3D. I am not sure if the upstream version of Volume Cartographer can deal with disparate 3d tiff chunks, either.
\nThe way VC3D currently works is that it deals with entire scroll volumes, like the ones we link to from the segmentation tutorial or the data page in the zarr format, that cover the entire scroll volume, rather than 3d tiff file chunks. The sample data we've provided for this competition is provided as 3d tiff chunks specifically for the surface prediction challenge, though VC3D is targetted more towards working with entire surface volumes and manual segmentation.
\nThat being said, I think I can add support for viewing tiff chunks pretty easily in the XY XZ YZ planes to do what you're asking. I'll put this on my todo list for tomorrow and will reply again once the changes are in.
", "rawMarkdown": "OK, so what you're trying to do is not currently supported by VC3D. I am not sure if the upstream version of Volume Cartographer can deal with disparate 3d tiff chunks, either. \n\nThe way VC3D currently works is that it deals with entire scroll volumes, like the ones we link to from the segmentation tutorial or the [data page](https://scrollprize.org/data_scrolls) in the zarr format, that cover the entire scroll volume, rather than 3d tiff file chunks. The sample data we've provided for this competition is provided as 3d tiff chunks specifically for the surface prediction challenge, though VC3D is targetted more towards working with entire surface volumes and manual segmentation.\n\nThat being said, I think I can add support for viewing tiff chunks pretty easily in the XY XZ YZ planes to do what you're asking. I'll put this on my todo list for tomorrow and will reply again once the changes are in." }, { "id": 3348489, "postDate": "2025-11-25T23:31:36.097Z", "content": "Thanks! I'm using 3D slicer to visualize the volumes. Be able to do it also in the VC3D would be nice to understand better the data. But, do you think 3D slicer is enough for understanding the challenge data?
", "rawMarkdown": "Thanks! I'm using 3D slicer to visualize the volumes. Be able to do it also in the VC3D would be nice to understand better the data. But, do you think 3D slicer is enough for understanding the challenge data? " }, { "id": 3349710, "postDate": "2025-11-26T22:55:49.840Z", "content": "3D slicer should be decent enough for understanding the structure of the subvolumes, but it can be nice to get a look at a full scroll! If you've got enough space locally i'd recommend at least taking a look at them in vc3d. If nothing else you could create labeled data to use in the competition
", "rawMarkdown": "3D slicer should be decent enough for understanding the structure of the subvolumes, but it can be nice to get a look at a full scroll! If you've got enough space locally i'd recommend at least taking a look at them in vc3d. If nothing else you could create labeled data to use in the competition " }, { "id": 3350314, "postDate": "2025-11-27T13:41:03.357Z", "content": "I don't have much experience with this type of data, so segmenting myself would probably just create noise. \nI will download a full volume and take a look, thanks!
", "rawMarkdown": "I don't have much experience with this type of data, so segmenting myself would probably just create noise. \nI will download a full volume and take a look, thanks!" } ] }, { "id": 3351415, "postDate": "2025-11-28T11:53:26.530Z", "content": "I wanted to understand the data too so I have created slicing visualization kernel for all three axis and if you run it you can interactivly browse any volume…\nhttps://www.kaggle.com/code/jirkaborovec/surface-eda-interactive-img-mask-3d-view
", "rawMarkdown": "I wanted to understand the data too so I have created slicing visualization kernel for all three axis and if you run it you can interactivly browse any volume...\nhttps://www.kaggle.com/code/jirkaborovec/surface-eda-interactive-img-mask-3d-view", "replies": [ { "id": 3351516, "postDate": "2025-11-28T13:26:00.520Z", "content": "Yes thank you! That's similar to visualize with 3D slicer 🙌
", "rawMarkdown": "Yes thank you! That's similar to visualize with 3D slicer 🙌" } ] } ] } ], "comments": [ { "id": 3344776, "author_name": "Forrest", "author_url": "", "post_date": "2025-11-22T23:46:26.433000", "content": "Are you using VC3D from https://github.com/ScrollPrize/villa/tree/main/volume-cartographer ? We don't support the upstream Volume Cartographer anymore. You'll need to piece together a volpkg directory from some segments, volume data, and a json configuration. Directions to do this can be found on the segmentation tutorial on our website: https://scrollprize.org/segmentation
", "votes": 0, "replies": [ { "id": 3348266, "author_name": "Andre Filipe Ferreira", "author_url": "", "post_date": "2025-11-25T17:46:05.163000", "content": "Thanks. I was trying to use the https://github.com/educelab/volume-cartographer. I will certainly take a look at the tutorial, thank you!
", "votes": 0, "replies": [ { "id": 3348387, "author_name": "", "author_url": "", "post_date": "2025-11-25T19:50:02.540000", "content": "", "votes": 0, "replies": [] } ] }, { "id": 3348388, "author_name": "Andre Filipe Ferreira", "author_url": "", "post_date": "2025-11-25T19:51:18.990000", "content": "I've tried to follow the tutorial. I've created the folder scroll1.volpkg, and created the folders normal_grids, paths, volumes and the file config.json. Inside of the config.json I have {\"materialthickness\":1.0,\"name\":\"Example\",\"version\":7}. Then, inside of the folder volumes I have two subfolders s1_uint8_ome and 050_entire_scroll1_ome. Each subfolder contains a .tif file 2290837.tif. In the first subfolder is the image and in the second is the segmentation, also in the .tif format. Then, inside of each folder I also have the meta.json file, with the content {\"height\":320,\"max\":65535.0,\"min\":0.0,\"name\":\"Example_raw\",\"slices\":320,\"type\":\"vol\",\"uuid\":\"20231117143551-s3_raw\",\"voxelsize\":1,\"width\":320, \"format\":\"tif\"}. The .volpkg is loaded correctly and the names appear correct, however, no image is shown. The planes are all white. Could you please assist me on this? Thank you!
OK, so what you're trying to do is not currently supported by VC3D. I am not sure if the upstream version of Volume Cartographer can deal with disparate 3d tiff chunks, either.
\nThe way VC3D currently works is that it deals with entire scroll volumes, like the ones we link to from the segmentation tutorial or the data page in the zarr format, that cover the entire scroll volume, rather than 3d tiff file chunks. The sample data we've provided for this competition is provided as 3d tiff chunks specifically for the surface prediction challenge, though VC3D is targetted more towards working with entire surface volumes and manual segmentation.
\nThat being said, I think I can add support for viewing tiff chunks pretty easily in the XY XZ YZ planes to do what you're asking. I'll put this on my todo list for tomorrow and will reply again once the changes are in.
", "votes": 0, "replies": [] }, { "id": 3348489, "author_name": "Andre Filipe Ferreira", "author_url": "", "post_date": "2025-11-25T23:31:36.097000", "content": "Thanks! I'm using 3D slicer to visualize the volumes. Be able to do it also in the VC3D would be nice to understand better the data. But, do you think 3D slicer is enough for understanding the challenge data?
", "votes": 0, "replies": [] }, { "id": 3349710, "author_name": "Sean Johnson_SP", "author_url": "", "post_date": "2025-11-26T22:55:49.840000", "content": "3D slicer should be decent enough for understanding the structure of the subvolumes, but it can be nice to get a look at a full scroll! If you've got enough space locally i'd recommend at least taking a look at them in vc3d. If nothing else you could create labeled data to use in the competition
", "votes": 0, "replies": [] }, { "id": 3350314, "author_name": "Andre Filipe Ferreira", "author_url": "", "post_date": "2025-11-27T13:41:03.357000", "content": "I don't have much experience with this type of data, so segmenting myself would probably just create noise. \nI will download a full volume and take a look, thanks!
", "votes": 0, "replies": [] } ] }, { "id": 3351415, "author_name": "Jirka", "author_url": "", "post_date": "2025-11-28T11:53:26.530000", "content": "I wanted to understand the data too so I have created slicing visualization kernel for all three axis and if you run it you can interactivly browse any volume…\nhttps://www.kaggle.com/code/jirkaborovec/surface-eda-interactive-img-mask-3d-view
", "votes": 0, "replies": [ { "id": 3351516, "author_name": "Andre Filipe Ferreira", "author_url": "", "post_date": "2025-11-28T13:26:00.520000", "content": "Yes thank you! That's similar to visualize with 3D slicer 🙌
", "votes": 0, "replies": [] } ] } ] } ], "raw_markdown_by_id": { "3343587": "I'm trying to visualize the dataset with the Volume Cartographer, but it requires .volpkg. The dataset isn't in this format. How can we solve this?\n\nThanks!", "3344776": "Are you using VC3D from https://github.com/ScrollPrize/villa/tree/main/volume-cartographer ? We don't support the upstream Volume Cartographer anymore. You'll need to piece together a volpkg directory from some segments, volume data, and a json configuration. Directions to do this can be found on the segmentation tutorial on our website: https://scrollprize.org/segmentation" } }