# Latest **URL:** https://forum.allencell.org/latest.md [Latest](https://forum.allencell.org/latest.md) · [Categories](https://forum.allencell.org/categories.md) · [Tags](https://forum.allencell.org/tags.md) --- ## [Western Blot background GFP bands-- how did you reduce this in WTC-11?](https://forum.allencell.org/t/western-blot-background-gfp-bands-how-did-you-reduce-this-in-wtc-11/796)
**Author:** [@MaggietheFuqua](https://forum.allencell.org/u/MaggietheFuqua)\ **Replies:** 1\ **Last updated:** [April 29, 2026, 5:12pm UTC](https://forum.allencell.org/t/western-blot-background-gfp-bands-how-did-you-reduce-this-in-wtc-11/796 "2026-04-29T17:12:32Z")
Hi there, From your Roberts et al., 2017 pub, your GFP Western Blots look very clean, but I’m using the same antibody specified and getting so many background bands in both WT and my mEGFP-tagged line lysates. Any chanc… --- ## [Endogenous base deletion ipsc generation](https://forum.allencell.org/t/endogenous-base-deletion-ipsc-generation/795)
**Author:** [@Souren](https://forum.allencell.org/u/Souren)\ **Replies:** 0\ **Last updated:** [March 31, 2026, 2:06pm UTC](https://forum.allencell.org/t/endogenous-base-deletion-ipsc-generation/795 "2026-03-31T14:06:18Z")
Hi , I want to perform some endogenous base deletion in H9 cells, can you suggest me some way out for that. Best Souren --- ## [FNet setup issues due to outdated dependencies – any updated version or Docker?](https://forum.allencell.org/t/fnet-setup-issues-due-to-outdated-dependencies-any-updated-version-or-docker/792)
**Author:** [@ines\_varona](https://forum.allencell.org/u/ines_varona)\ **Replies:** 5\ **Last updated:** [March 25, 2026, 11:31pm UTC](https://forum.allencell.org/t/fnet-setup-issues-due-to-outdated-dependencies-any-updated-version-or-docker/792 "2026-03-25T23:31:18Z")
Hi everyone, I am currently running some experiments and would like to compare my results with outputs obtained using the FNet architecture. However, while setting up the environment and installing the required depende… --- ## [Finding Specific Track IDs in Vol-E](https://forum.allencell.org/t/finding-specific-track-ids-in-vol-e/794)
**Author:** [@swalsh](https://forum.allencell.org/u/swalsh)\ **Replies:** 1\ **Last updated:** [March 23, 2026, 3:49am UTC](https://forum.allencell.org/t/finding-specific-track-ids-in-vol-e/794 "2026-03-23T03:49:43Z")
Hi, we have analyzed a bunch of data through TFE, and it would be nice to verify the 3D images in Vol-E. We have a list of track IDs and time stamps, and we would like to zoom in to capture images of the cells at particu… --- ## [Drug perturbation pilot study metadata is missing](https://forum.allencell.org/t/drug-perturbation-pilot-study-metadata-is-missing/788)
**Author:** [@UBio1600](https://forum.allencell.org/u/UBio1600)\ **Replies:** 3\ **Last updated:** [March 1, 2026, 1:53pm UTC](https://forum.allencell.org/t/drug-perturbation-pilot-study-metadata-is-missing/788 "2026-03-01T13:53:26Z")
Hi! I am exploring the data in Drug perturbation pilot study - ALLEN CELL EXPLORER for drug function study. However, the metadata provided in Download cell data: images, genomics, features - ALLEN CELL EXPLORER is not pe… --- ## [Issues with dCAS9-BFP line](https://forum.allencell.org/t/issues-with-dcas9-bfp-line/787)
**Author:** [@marcomhefti](https://forum.allencell.org/u/marcomhefti)\ **Replies:** 1\ **Last updated:** [February 19, 2026, 7:37pm UTC](https://forum.allencell.org/t/issues-with-dcas9-bfp-line/787 "2026-02-19T19:37:34Z")
I am writing regarding the dCas9 cell line (Cat. No. AICS-0090-391) that we recently purchased from the Coriell Institute. We tested the cells for the BFP tag but were unable to detect any signal using our Cytation5 imag… --- ## [Pictures of Healthy vs Unhealthy hiPSC colonies](https://forum.allencell.org/t/pictures-of-healthy-vs-unhealthy-hipsc-colonies/26)
**Author:** [@cells](https://forum.allencell.org/u/cells)\ **Replies:** 5\ **Last updated:** [January 20, 2026, 11:03pm UTC](https://forum.allencell.org/t/pictures-of-healthy-vs-unhealthy-hipsc-colonies/26 "2026-01-20T23:03:54Z")
How should healthy iPSC colonies look? What characteristics define a bad colony? --- ## [iPSC line AICS-0090-391 adipogenic differentiation](https://forum.allencell.org/t/ipsc-line-aics-0090-391-adipogenic-differentiation/785)
**Author:** [@Carolinepancera](https://forum.allencell.org/u/Carolinepancera)\ **Replies:** 0\ **Last updated:** [November 19, 2025, 10:00pm UTC](https://forum.allencell.org/t/ipsc-line-aics-0090-391-adipogenic-differentiation/785 "2025-11-19T22:00:38Z")
I am currently planning experiments involving the iPSC line AICS-0090-391 (WTC-CLYBL-dCas9-TagBFP-KRAB-cl391). I would like to know whether this specific line has been previously used or validated for adipogenic differe… --- ## [Brain and body donation to Allen Institute to support specified research](https://forum.allencell.org/t/brain-and-body-donation-to-allen-institute-to-support-specified-research/781)
**Author:** [@stevenentanglement](https://forum.allencell.org/u/stevenentanglement)\ **Replies:** 1\ **Last updated:** [November 13, 2025, 10:41pm UTC](https://forum.allencell.org/t/brain-and-body-donation-to-allen-institute-to-support-specified-research/781 "2025-11-13T22:41:41Z")
I am 75. I desire to donate my brain and the rest of my body immediately after I die to scientists and a laboratory in order to advance my goals. Scientists, engineers and a lab at Allen Insitute would be best, of cour… --- ## [WTC-11 Genome Sequence in the UCSC Browser](https://forum.allencell.org/t/wtc-11-genome-sequence-in-the-ucsc-browser/777)
**Author:** [@AbhiRBio](https://forum.allencell.org/u/AbhiRBio)\ **Replies:** 3\ **Last updated:** [October 8, 2025, 4:54am UTC](https://forum.allencell.org/t/wtc-11-genome-sequence-in-the-ucsc-browser/777 "2025-10-08T04:54:34Z")
While trying to view the WTC-11 parental short read genome sequence and variants in the UCSC genome browser, I have been running into an error loading the hub.txt file (image attached), on both Mac and Windows browsers. … --- ## [Thaw, expand and maintain MONO-ALLELIC mEGFP-TAGGED SOX2 cells in E8+ flex medium (Invitrogen) on Vitronectin-N coated wells](https://forum.allencell.org/t/thaw-expand-and-maintain-mono-allelic-megfp-tagged-sox2-cells-in-e8-flex-medium-invitrogen-on-vitronectin-n-coated-wells/771)
**Author:** [@leahpeng](https://forum.allencell.org/u/leahpeng)\ **Replies:** 1\ **Last updated:** [July 30, 2025, 8:09pm UTC](https://forum.allencell.org/t/thaw-expand-and-maintain-mono-allelic-megfp-tagged-sox2-cells-in-e8-flex-medium-invitrogen-on-vitronectin-n-coated-wells/771 "2025-07-30T20:09:44Z")
Hi, We would like to thaw, expand and maintain MONO-ALLELIC mEGFP-TAGGED SOX2 cells in E8+ flex medium (Invitrogen) on Vitronectin-N coated wells, which is different method comparing to the protocol provided by the Cori… --- ## [Recreating gif style figure on Spherical Harmonics read me](https://forum.allencell.org/t/recreating-gif-style-figure-on-spherical-harmonics-read-me/766)
**Author:** [@msforman](https://forum.allencell.org/u/msforman)\ **Replies:** 1\ **Last updated:** [June 26, 2025, 8:30pm UTC](https://forum.allencell.org/t/recreating-gif-style-figure-on-spherical-harmonics-read-me/766 "2025-06-26T20:30:39Z")
I am looking to recreate this figure and was curious what tools were used to generate it, and how the ‘error’ is found/calculated here (MSE?) Thank you! --- ## [Tips for reducing non-specific antibody binding in WTC-11 cells on coated glass](https://forum.allencell.org/t/tips-for-reducing-non-specific-antibody-binding-in-wtc-11-cells-on-coated-glass/761)
**Author:** [@MaggietheFuqua](https://forum.allencell.org/u/MaggietheFuqua)\ **Replies:** 0\ **Last updated:** [April 23, 2025, 7:54pm UTC](https://forum.allencell.org/t/tips-for-reducing-non-specific-antibody-binding-in-wtc-11-cells-on-coated-glass/761 "2025-04-23T19:54:02Z")
Hello! I’ve been optimizing antibodies for IF using the WTC-11 cells and have utilized both Matrigel and Vitronectin, but am still seeing non-specific binding in my secondary-only controls in both cell-containing and ce… --- ## [Culturing hiPSC and Other Cell Lines in Same Lab Space](https://forum.allencell.org/t/culturing-hipsc-and-other-cell-lines-in-same-lab-space/760)
**Author:** [@drlatham77](https://forum.allencell.org/u/drlatham77)\ **Replies:** 1\ **Last updated:** [April 2, 2025, 8:51pm UTC](https://forum.allencell.org/t/culturing-hipsc-and-other-cell-lines-in-same-lab-space/760 "2025-04-02T20:51:22Z")
Hello! Our lab has a single small space for culturing cells. We have been using the Allen ihPSC cells and are looking into bringing in another cell line, 3T3. I know that HeLa cells have issues with ‘jumping’ between cu… --- ## [AICS-0126-068:WTC-mEGFP-CDH5 and AICS-0126-041:WTC-mEGFP-CDH5](https://forum.allencell.org/t/aics-0126-068-wtc-megfp-cdh5-and-aics-0126-041-wtc-megfp-cdh5/758)
**Author:** [@Tatjana](https://forum.allencell.org/u/Tatjana)\ **Replies:** 1\ **Last updated:** [March 20, 2025, 8:26pm UTC](https://forum.allencell.org/t/aics-0126-068-wtc-megfp-cdh5-and-aics-0126-041-wtc-megfp-cdh5/758 "2025-03-20T20:26:22Z")
Hi Allen team, We are thinking to purchase a VE-cadherin tagged iPSC line and would like to ask you whether the monoallelic (AICS-0126-068) or biallelic (AICS-0126-041) one would be the most favorable to visualize the e… --- ## [(AICS-0074-026) MONO-ALLELIC mEGFP-TAGGED SOX hiPSCs Thawing/freezing question](https://forum.allencell.org/t/aics-0074-026-mono-allelic-megfp-tagged-sox-hipscs-thawing-freezing-question/755)
**Author:** [@MariaEleni](https://forum.allencell.org/u/MariaEleni)\ **Replies:** 2\ **Last updated:** [March 20, 2025, 11:39am UTC](https://forum.allencell.org/t/aics-0074-026-mono-allelic-megfp-tagged-sox-hipscs-thawing-freezing-question/755 "2025-03-20T11:39:35Z")
Hello everyone, we recently ordered MONO-ALLELIC mEGFP-TAGGED SOX catalog ID AICS-0074-026. We have technical questions regarding handling the cells right after thawing and when freezing: Can the cells be directly tha… --- ## [Cvapipe\_analysis, cannot run test case (shape analysis on 300 cells)](https://forum.allencell.org/t/cvapipe-analysis-cannot-run-test-case-shape-analysis-on-300-cells/757)
**Author:** [@lucas.philipp1](https://forum.allencell.org/u/lucas.philipp1)\ **Replies:** 1\ **Last updated:** [March 19, 2025, 11:52pm UTC](https://forum.allencell.org/t/cvapipe-analysis-cannot-run-test-case-shape-analysis-on-300-cells/757 "2025-03-19T23:52:21Z")
Description A clear description of the bug Successfully installed cvapipe\_analysis, although I had to use Python 3.9 instead of Python 3.8 as recommended. I tried running cvapipe\_analysis loaddata run --test, but the th… --- ## [Protocol for Parental Cell Line (GM25256)](https://forum.allencell.org/t/protocol-for-parental-cell-line-gm25256/748)
**Author:** [@llachowski](https://forum.allencell.org/u/llachowski)\ **Replies:** 1\ **Last updated:** [February 17, 2025, 10:12pm UTC](https://forum.allencell.org/t/protocol-for-parental-cell-line-gm25256/748 "2025-02-17T22:12:38Z")
The protocol you provide for your cell lines (GM25256\*l) is slightly different from the protocol provided for the parental line (GM2526). My lab is interested in purchasing and culturing both your cell lines and the pare… --- ## [AICS-0037-172-MONO-ALLELIC mEGFP-TAGGED TNNI iPSCs RFP Signal](https://forum.allencell.org/t/aics-0037-172-mono-allelic-megfp-tagged-tnni-ipscs-rfp-signal/742)
**Author:** [@Mani1830](https://forum.allencell.org/u/Mani1830)\ **Replies:** 1\ **Last updated:** [February 4, 2025, 1:06am UTC](https://forum.allencell.org/t/aics-0037-172-mono-allelic-megfp-tagged-tnni-ipscs-rfp-signal/742 "2025-02-04T01:06:18Z")
Hi team, We differentiated the hiPSCs into cardiomyocytes and we observed that the RFP was observed but not GFP expression. Moreover, we didn’t observe the beating of the cardiomyocytes. Any suggestion would be highly a… --- ## [Hypothalmus tissues not included in the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3)](https://forum.allencell.org/t/hypothalmus-tissues-not-included-in-the-allen-mouse-brain-common-coordinate-framework-version-3-ccfv3/738)
**Author:** [@MouseDatabase](https://forum.allencell.org/u/MouseDatabase)\ **Replies:** 2\ **Last updated:** [January 29, 2025, 6:32pm UTC](https://forum.allencell.org/t/hypothalmus-tissues-not-included-in-the-allen-mouse-brain-common-coordinate-framework-version-3-ccfv3/738 "2025-01-29T18:32:37Z")
I am looking at the GEO entry (GSE246717) for the scRNA-seq data in the Allen Brain Cell Atlas. There are several hypothalmic tissue samples identified by abbreviations not used in the Allen Mouse Brain Common Coordinate… --- ## [Advice of Lipofectamine STEM protocol](https://forum.allencell.org/t/advice-of-lipofectamine-stem-protocol/735)
**Author:** [@AbhiRBio](https://forum.allencell.org/u/AbhiRBio)\ **Replies:** 1\ **Last updated:** [December 4, 2024, 5:27pm UTC](https://forum.allencell.org/t/advice-of-lipofectamine-stem-protocol/735 "2024-12-04T17:27:23Z")
Hi! I recently tried to transfect WTC10 stem cells with a gene under the EF1a promoter. ~30k cells were seeded per well of a CellVisC4-1.5H-N chambered slide coated with vitronectin, in mTeSR+ medium with 1X RevitaCell … --- ## [Single cell cluster naming](https://forum.allencell.org/t/single-cell-cluster-naming/734)
**Author:** [@sc\_confusion](https://forum.allencell.org/u/sc_confusion)\ **Replies:** 1\ **Last updated:** [November 27, 2024, 5:47pm UTC](https://forum.allencell.org/t/single-cell-cluster-naming/734 "2024-11-27T17:47:47Z")
I know in general the Allen institute does a lot of careful thought in naming single cell clusters, but I am seeing a general trend with a lot of single cell papers from other places and am trying to get a better underst… --- ## [Demethylating haldol affected genes](https://forum.allencell.org/t/demethylating-haldol-affected-genes/730)
**Author:** [@rcdennis](https://forum.allencell.org/u/rcdennis)\ **Replies:** 4\ **Last updated:** [November 12, 2024, 7:06pm UTC](https://forum.allencell.org/t/demethylating-haldol-affected-genes/730 "2024-11-12T19:06:17Z")
How can I gain access to sequence methylation and CrisprOn to restore affected genes? --- ## [Image viewer error classic segmentation jupyter notebook](https://forum.allencell.org/t/image-viewer-error-classic-segmentation-jupyter-notebook/455)
**Author:** [@AidanF](https://forum.allencell.org/u/AidanF)\ **Replies:** 4\ **Last updated:** [August 15, 2024, 10:09pm UTC](https://forum.allencell.org/t/image-viewer-error-classic-segmentation-jupyter-notebook/455 "2024-08-15T22:09:05Z")
Hi All, New error experienced when running the look up table demo via jupyter notebook (through anaconda). During the loading the data step I get the following error: Failed to parse XML for the provided file. Error: … --- ## [How to keep cardiac differentiated cells from coming apart lifting from well](https://forum.allencell.org/t/how-to-keep-cardiac-differentiated-cells-from-coming-apart-lifting-from-well/724)
**Author:** [@hartw006](https://forum.allencell.org/u/hartw006)\ **Replies:** 1\ **Last updated:** [July 30, 2024, 4:18pm UTC](https://forum.allencell.org/t/how-to-keep-cardiac-differentiated-cells-from-coming-apart-lifting-from-well/724 "2024-07-30T16:18:19Z")
How do you to keep cardiac differentiated cells from coming apart and lifting from well? My cells beat so hard they do not last that long, a month a most. --- ## [Evaluating morphology of hiPS colonies](https://forum.allencell.org/t/evaluating-morphology-of-hips-colonies/721)
**Author:** [@AbhiRBio](https://forum.allencell.org/u/AbhiRBio)\ **Replies:** 1\ **Last updated:** [July 25, 2024, 4:06am UTC](https://forum.allencell.org/t/evaluating-morphology-of-hips-colonies/721 "2024-07-25T04:06:22Z")
Hi! Would it be possible to receive an opinion on the general morphology/health of some hiPSC’s which we are maintaining? --- ## [Drug perturbation single cell segmentation](https://forum.allencell.org/t/drug-perturbation-single-cell-segmentation/719)
**Author:** [@MattDV](https://forum.allencell.org/u/MattDV)\ **Replies:** 1\ **Last updated:** [July 2, 2024, 3:58am UTC](https://forum.allencell.org/t/drug-perturbation-single-cell-segmentation/719 "2024-07-02T03:58:16Z")
Hi, are there any single cell segmentations available for the drug perturbation pilot study? --- ## [How to access cell lines](https://forum.allencell.org/t/how-to-access-cell-lines/717)
**Author:** [@SaraA1](https://forum.allencell.org/u/SaraA1)\ **Replies:** 1\ **Last updated:** [June 20, 2024, 3:55pm UTC](https://forum.allencell.org/t/how-to-access-cell-lines/717 "2024-06-20T15:55:13Z")
Hi! I am new here, and was wondering how I could access these newly generated cell lines Disease Collection Cell Catalog - ALLEN CELL EXPLORER ? Many thanks Sara --- ## [Is there any timelapse microscopy data for fluorescently tagged hiPSCs available for download?](https://forum.allencell.org/t/is-there-any-timelapse-microscopy-data-for-fluorescently-tagged-hipscs-available-for-download/707)
**Author:** [@cell](https://forum.allencell.org/u/cell)\ **Replies:** 1\ **Last updated:** [May 16, 2024, 7:45pm UTC](https://forum.allencell.org/t/is-there-any-timelapse-microscopy-data-for-fluorescently-tagged-hipscs-available-for-download/707 "2024-05-16T19:45:21Z")
Hi, I am new here and looking to see if there is any timelapse microscopy data available for download for the fluorescently tagged hiPSC lines. For example, is the microscopy data available for the compiled movies of som… --- ## [Facing Problems while working with AICSImage package for CZI files](https://forum.allencell.org/t/facing-problems-while-working-with-aicsimage-package-for-czi-files/690)
**Author:** [@dnadeem57](https://forum.allencell.org/u/dnadeem57)\ **Replies:** 4\ **Last updated:** [April 11, 2024, 5:16pm UTC](https://forum.allencell.org/t/facing-problems-while-working-with-aicsimage-package-for-czi-files/690 "2024-04-11T17:16:35Z")
Hi All, I am working with LLSM movies as CZI files. The movies have 3 channels and are pretty large so I am using delayed image reading from the AICSImage package. The code is as follows. I am trying to access one time… [Next page](https://forum.allencell.org/latest.md?page=1)