| _version_ | 1866902198978347008 |
|---|---|
| author | Ali Khan Dhananjhay Bansal (Djay) Karl5766 |
| author_facet | Ali Khan Dhananjhay Bansal (Djay) Karl5766 |
| contents | <h2>What's Changed</h2> <ul> <li>Improve SPIMquant directory structure by @Karl5766 in https://github.com/khanlab/SPIMquant/pull/14</li> <li>Stains from ome-zarr, and Eed atlas labels by @akhanf in https://github.com/khanlab/SPIMquant/pull/16</li> <li>threshold-based segmentation, coiled for N4/thresholding, BIDS app CLI, gubra and marmoset template, by @akhanf in https://github.com/khanlab/SPIMquant/pull/18</li> <li>Various fixes to clean-up CLI, and get segmentation working on local compute (without coiled) by @akhanf in https://github.com/khanlab/SPIMquant/pull/19</li> <li>add gubra files (download tar), other cleanup by @akhanf in https://github.com/khanlab/SPIMquant/pull/20</li> <li>Turone by @akhanf in https://github.com/khanlab/SPIMquant/pull/21</li> <li>add missing upath dependency by @akhanf in https://github.com/khanlab/SPIMquant/pull/22</li> <li>change default work path by @akhanf in https://github.com/khanlab/SPIMquant/pull/23</li> <li>utils fix by @akhanf in https://github.com/khanlab/SPIMquant/pull/25</li> <li>another fix for cloud storage uris by @akhanf in https://github.com/khanlab/SPIMquant/pull/26</li> <li>couple more pesky fixes for storage creds by @akhanf in https://github.com/khanlab/SPIMquant/pull/27</li> <li>initial version of lightsheet-mri intra-subject registration by @akhanf in https://github.com/khanlab/SPIMquant/pull/28</li> <li>add Ngo atlas to ABAv3 template by @akhanf in https://github.com/khanlab/SPIMquant/pull/29</li> <li>Pixi refactor, zarrnii 0.3.0 (uses zarr v3), remove containers by @akhanf in https://github.com/khanlab/SPIMquant/pull/31</li> <li>updates and fixes for segmentation workflows by @akhanf in https://github.com/khanlab/SPIMquant/pull/30</li> <li>Pipeline cleanup by @Dhananjhay in https://github.com/khanlab/SPIMquant/pull/32</li> <li>fixes for zarr with no z downsampling by @akhanf in https://github.com/khanlab/SPIMquant/pull/33</li> <li>use temp() on more files by @akhanf in https://github.com/khanlab/SPIMquant/pull/34</li> <li>Add --template-crop CLI option for hemisphere-specific template registration by @Copilot in https://github.com/khanlab/SPIMquant/pull/36</li> <li>add downsampled dataset by @akhanf in https://github.com/khanlab/SPIMquant/pull/37</li> <li>Clean up extraneous rules, scripts, notebooks, and config parameters not used in default workflow by @Copilot in https://github.com/khanlab/SPIMquant/pull/38</li> <li>Refactor for updates to zarrnii, plugins etc by @akhanf in https://github.com/khanlab/SPIMquant/pull/39</li> <li>Bump the dependencies group with 2 updates by @dependabot[bot] in https://github.com/khanlab/SPIMquant/pull/40</li> <li>Update documentation to use pixi instead of pip and singularity for installation by @Copilot in https://github.com/khanlab/SPIMquant/pull/42</li> <li>Add GitHub Copilot instructions for SPIMquant development by @Copilot in https://github.com/khanlab/SPIMquant/pull/43</li> </ul> <h2>New Contributors</h2> <ul> <li>@Karl5766 made their first contribution in https://github.com/khanlab/SPIMquant/pull/14</li> <li>@Dhananjhay made their first contribution in https://github.com/khanlab/SPIMquant/pull/32</li> <li>@Copilot made their first contribution in https://github.com/khanlab/SPIMquant/pull/36</li> <li>@dependabot[bot] made their first contribution in https://github.com/khanlab/SPIMquant/pull/40</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/khanlab/SPIMquant/compare/v0.1.0-alpha2...v0.2.0-alpha1</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17208742 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | khanlab/SPIMquant: v0.2.0-alpha1 Ali Khan Dhananjhay Bansal (Djay) Karl5766 <h2>What's Changed</h2> <ul> <li>Improve SPIMquant directory structure by @Karl5766 in https://github.com/khanlab/SPIMquant/pull/14</li> <li>Stains from ome-zarr, and Eed atlas labels by @akhanf in https://github.com/khanlab/SPIMquant/pull/16</li> <li>threshold-based segmentation, coiled for N4/thresholding, BIDS app CLI, gubra and marmoset template, by @akhanf in https://github.com/khanlab/SPIMquant/pull/18</li> <li>Various fixes to clean-up CLI, and get segmentation working on local compute (without coiled) by @akhanf in https://github.com/khanlab/SPIMquant/pull/19</li> <li>add gubra files (download tar), other cleanup by @akhanf in https://github.com/khanlab/SPIMquant/pull/20</li> <li>Turone by @akhanf in https://github.com/khanlab/SPIMquant/pull/21</li> <li>add missing upath dependency by @akhanf in https://github.com/khanlab/SPIMquant/pull/22</li> <li>change default work path by @akhanf in https://github.com/khanlab/SPIMquant/pull/23</li> <li>utils fix by @akhanf in https://github.com/khanlab/SPIMquant/pull/25</li> <li>another fix for cloud storage uris by @akhanf in https://github.com/khanlab/SPIMquant/pull/26</li> <li>couple more pesky fixes for storage creds by @akhanf in https://github.com/khanlab/SPIMquant/pull/27</li> <li>initial version of lightsheet-mri intra-subject registration by @akhanf in https://github.com/khanlab/SPIMquant/pull/28</li> <li>add Ngo atlas to ABAv3 template by @akhanf in https://github.com/khanlab/SPIMquant/pull/29</li> <li>Pixi refactor, zarrnii 0.3.0 (uses zarr v3), remove containers by @akhanf in https://github.com/khanlab/SPIMquant/pull/31</li> <li>updates and fixes for segmentation workflows by @akhanf in https://github.com/khanlab/SPIMquant/pull/30</li> <li>Pipeline cleanup by @Dhananjhay in https://github.com/khanlab/SPIMquant/pull/32</li> <li>fixes for zarr with no z downsampling by @akhanf in https://github.com/khanlab/SPIMquant/pull/33</li> <li>use temp() on more files by @akhanf in https://github.com/khanlab/SPIMquant/pull/34</li> <li>Add --template-crop CLI option for hemisphere-specific template registration by @Copilot in https://github.com/khanlab/SPIMquant/pull/36</li> <li>add downsampled dataset by @akhanf in https://github.com/khanlab/SPIMquant/pull/37</li> <li>Clean up extraneous rules, scripts, notebooks, and config parameters not used in default workflow by @Copilot in https://github.com/khanlab/SPIMquant/pull/38</li> <li>Refactor for updates to zarrnii, plugins etc by @akhanf in https://github.com/khanlab/SPIMquant/pull/39</li> <li>Bump the dependencies group with 2 updates by @dependabot[bot] in https://github.com/khanlab/SPIMquant/pull/40</li> <li>Update documentation to use pixi instead of pip and singularity for installation by @Copilot in https://github.com/khanlab/SPIMquant/pull/42</li> <li>Add GitHub Copilot instructions for SPIMquant development by @Copilot in https://github.com/khanlab/SPIMquant/pull/43</li> </ul> <h2>New Contributors</h2> <ul> <li>@Karl5766 made their first contribution in https://github.com/khanlab/SPIMquant/pull/14</li> <li>@Dhananjhay made their first contribution in https://github.com/khanlab/SPIMquant/pull/32</li> <li>@Copilot made their first contribution in https://github.com/khanlab/SPIMquant/pull/36</li> <li>@dependabot[bot] made their first contribution in https://github.com/khanlab/SPIMquant/pull/40</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/khanlab/SPIMquant/compare/v0.1.0-alpha2...v0.2.0-alpha1</p> |
| title | khanlab/SPIMquant: v0.2.0-alpha1 |
| url | https://doi.org/10.5281/zenodo.17208742 |