# Iterative Deep Learning Workflow **URL:** \ **Category:** Segmenter\ **Created:** [August 2, 2021, 2:29pm UTC](https://forum.allencell.org/t/iterative-deep-learning-workflow/340 "2021-08-02T14:29:28Z")\ **Posts on this page:** 11\ **Page:** 1
**Author:** ![RexH](https://avatars.discourse-cdn.com/v4/letter/r/c37758/32.png) [@RexH](https://forum.allencell.org/u/RexH)\ **Post date:** [August 2, 2021, 2:29pm UTC](https://forum.allencell.org/t/iterative-deep-learning-workflow/340/1 "2021-08-02T14:29:28Z")
Hello Allen Segmentation Developers, I am trying to use the Iterative Deep Learning Workflow on a Windows 10 operating system utilizing a Bash Shell with an Ubuntu command window (Windows Subsystem for Linux) (version 1). ![image](https://canada1.discourse-cdn.com/flex027/uploads/allencell/original/1X/8b607fce6dc297f4986e51186c5666f6f32e3130.png) I have followed the aics-ml-segmentation / READ.md instructions exactly. At the install Pytorch setting I chose Stable (1.9.0), Linux, Conda, Python, CPU. I cloned everything and I tried to use the curator\_sorting help feature. The first error code I received was module not found error: no module named ‘aicssegmentation’. ![image](https://canada1.discourse-cdn.com/flex027/uploads/allencell/original/1X/f4560210dd73a64a4107651748a98ae05c0aa70c.jpeg) I then pip installed aicssegmentation. I tried to use the curator\_sorting help function again and received this error. ![image](https://canada1.discourse-cdn.com/flex027/uploads/allencell/original/1X/cb26f93d44b6bba0c88a5b46f19e233c8f9167de.jpeg) I can get the Classic Image Segmentation Workflow to work properly on Windows Subsystem for Linux, In addition, we can install the Iterative Deep Learning Workflow on a Mac and can run the curator\_sorting help function without an error. However, we can cannot we get the above error on the Ubuntu command window (Windows Subsystem for Linux). Additional information you might need: pip show aicssegmentation ![image](https://canada1.discourse-cdn.com/flex027/uploads/allencell/original/1X/ee3d6f77ab829fb8f6425957f6d5573d0ddc6bd4.png) pip show aicsmlsegment ![image](https://canada1.discourse-cdn.com/flex027/uploads/allencell/original/1X/ef255ef5d9a3cfb0bf8d97129e1a037c9cc0c79e.png) Please advise me on what I might be missing or need to install to make the mlsegmenter environment work. Best regards, RexH ---
**Author:** ![jianxu\_chen](https://avatars.discourse-cdn.com/v4/letter/j/85f322/32.png) [@jianxu\_chen](https://forum.allencell.org/u/jianxu_chen)\ **Post date:** [August 6, 2021, 6:39am UTC](https://forum.allencell.org/t/iterative-deep-learning-workflow/340/2 "2021-08-06T06:39:00Z")
Hello @RexH , Thanks for reporting the missing package `aicssegmentation` in the requirement. I have fixed this in the latest version. Regarding your errors related to `TkAgg`, I would suggest you to try running this in Anaconda prompt for Windows. Follow the guide here: [Installing on Windows — Anaconda documentation](https://docs.anaconda.com/anaconda/install/windows/) I just tried one more time `curator_sorting -h` . It works well within Anaconda prompt. Let me if you have more issues. Thanks, Jianxu ---
**Author:** ![RexH](https://avatars.discourse-cdn.com/v4/letter/r/c37758/32.png) [@RexH](https://forum.allencell.org/u/RexH)\ **Post date:** [August 12, 2021, 4:55pm UTC](https://forum.allencell.org/t/iterative-deep-learning-workflow/340/3 "2021-08-12T16:55:35Z")
Hello Jianxu\_Chen, I want to thank you for your previous post on how to resolve our TKAgg error. Your suggestion worked very well. I am posting again as I am unable to get the interface to pop up showing specified slices and a max projection within the curator\_sorting. I have included screen shots of the images from Fiji that I am using and a screen shot of the Anaconda prompt for Windows. When I press enter this is what happens in the highlighted red rectangle. ![image](https://canada1.discourse-cdn.com/flex027/uploads/allencell/original/1X/888a1622c5cfc269d8faba9ec2ef6e98cd5e73d4.png) ![image](https://canada1.discourse-cdn.com/flex027/uploads/allencell/original/1X/b46259032e0dff08b7b266bf155d491f71af0250.png) Any suggestions you may have would be welcome. Best regards, RexH ---
**Author:** ![RexH](https://avatars.discourse-cdn.com/v4/letter/r/c37758/32.png) [@RexH](https://forum.allencell.org/u/RexH)\ **Post date:** [August 19, 2021, 7:27pm UTC](https://forum.allencell.org/t/iterative-deep-learning-workflow/340/4 "2021-08-19T19:27:31Z")
Hello @jianxu_chen, I want to thank you for your previous post on how to resolve our TKAgg error. Your suggestion worked very well. I am reposting a previous question as I am wondering if it might not have alerted you to the post. I am unable to get the interface to pop up showing specified slices and a max projection within the curator\_sorting. I have included screen shots of the images from Fiji that I am using and a screen shot of the Anaconda prompt for Windows. When I press enter this is what happens in the highlighted red rectangle. ![image](https://canada1.discourse-cdn.com/flex027/uploads/allencell/original/1X/888a1622c5cfc269d8faba9ec2ef6e98cd5e73d4.png) ![image](https://canada1.discourse-cdn.com/flex027/uploads/allencell/original/1X/b46259032e0dff08b7b266bf155d491f71af0250.png) Any suggestions you may have would be welcome. Best regards, RexH ---
**Author:** ![jianxu\_chen](https://avatars.discourse-cdn.com/v4/letter/j/85f322/32.png) [@jianxu\_chen](https://forum.allencell.org/u/jianxu_chen)\ **Post date:** [August 20, 2021, 3:32pm UTC](https://forum.allencell.org/t/iterative-deep-learning-workflow/340/5 "2021-08-20T15:32:49Z")
Dear @RexH , Sorry for the late reply. This looks very strange. I will try to reproduce this error on my end and get back to you asap. Thanks, Jianxu ---
**Author:** ![jianxu\_chen](https://avatars.discourse-cdn.com/v4/letter/j/85f322/32.png) [@jianxu\_chen](https://forum.allencell.org/u/jianxu_chen)\ **Post date:** [August 20, 2021, 3:34pm UTC](https://forum.allencell.org/t/iterative-deep-learning-workflow/340/6 "2021-08-20T15:34:14Z")
hi @RexH , May I ask what will you see in the `curator_sorting_record.csv`? Also, can you double check the raw `.tiff` files exist under the directory you used for `--raw_path`? ---
**Author:** ![RexH](https://avatars.discourse-cdn.com/v4/letter/r/c37758/32.png) [@RexH](https://forum.allencell.org/u/RexH)\ **Post date:** [August 20, 2021, 3:59pm UTC](https://forum.allencell.org/t/iterative-deep-learning-workflow/340/7 "2021-08-20T15:59:22Z")
Hi @jianxu_chen, This is the output to the curator\_sorting\_record.csv ![image](https://canada1.discourse-cdn.com/flex027/uploads/allencell/original/1X/77e325995dd14d68603532a274602c39835b7943.png) This is inside the directory for the --raw\_path. ![image](https://canada1.discourse-cdn.com/flex027/uploads/allencell/original/1X/65006f37536553a6076e39672cabf0b1b50bb4b1.png) I am sending you an image of the properties just to verify that it is a .tiff image. ![image](https://canada1.discourse-cdn.com/flex027/uploads/allencell/original/1X/c70474e1ec933fb329d2001a397ae63f2752305e.png) Thank you, RexH ---
**Author:** ![jianxu\_chen](https://avatars.discourse-cdn.com/v4/letter/j/85f322/32.png) [@jianxu\_chen](https://forum.allencell.org/u/jianxu_chen)\ **Post date:** [August 20, 2021, 4:16pm UTC](https://forum.allencell.org/t/iterative-deep-learning-workflow/340/8 "2021-08-20T16:16:39Z")
Looks like your file extention is .tif instead of .tiff So, all you need to do is to change --data\_type to .tif ---
**Author:** ![RexH](https://avatars.discourse-cdn.com/v4/letter/r/c37758/32.png) [@RexH](https://forum.allencell.org/u/RexH)\ **Post date:** [August 20, 2021, 5:18pm UTC](https://forum.allencell.org/t/iterative-deep-learning-workflow/340/9 "2021-08-20T17:18:24Z")
Hi @jianxu_chen, I have changed all the files to all be .tif as the batch\_processing from the classic segmenter creates .tiff files. Now when I run the curator\_sorting I receive these error codes. ![image](https://canada1.discourse-cdn.com/flex027/uploads/allencell/original/1X/b5b535b55ba89813584b21f46391de2624bd2fa8.png) This is different than what I was receiving before which was ![image](https://canada1.discourse-cdn.com/flex027/uploads/allencell/original/1X/b46259032e0dff08b7b266bf155d491f71af0250.png) Regards, RexH ---
**Author:** ![jianxu\_chen](https://avatars.discourse-cdn.com/v4/letter/j/85f322/32.png) [@jianxu\_chen](https://forum.allencell.org/u/jianxu_chen)\ **Post date:** [August 20, 2021, 6:32pm UTC](https://forum.allencell.org/t/iterative-deep-learning-workflow/340/10 "2021-08-20T18:32:42Z")
Hi @RexH , So sorry if my previous message was confusing. To be clear - DO not change the segmentation files. `.tiff` is correct - When you type in the command, one of the things you type in is `--data_type`, currently, your command has `--data_type .tiff`. Since you raw images are `.tif`, you need to do `--data_type .tif` Thanks, Jianxu ---
**Author:** ![RexH](https://avatars.discourse-cdn.com/v4/letter/r/c37758/32.png) [@RexH](https://forum.allencell.org/u/RexH)\ **Post date:** [August 20, 2021, 7:02pm UTC](https://forum.allencell.org/t/iterative-deep-learning-workflow/340/11 "2021-08-20T19:02:19Z")
Hi @jianxu_chen, Thank you so much for your help! It is working now. I was very happy to see the interface populate. Moving on to the next step of the process. Regards, RexH