# Latest **URL:** https://forum.allencell.org/latest.md?page=1 [Latest](https://forum.allencell.org/latest.md) · [Categories](https://forum.allencell.org/categories.md) · [Tags](https://forum.allencell.org/tags.md) **Page:** 2 --- ## [Found way around not well formed error and itkwidgets error, Classical Segmenter](https://forum.allencell.org/t/found-way-around-not-well-formed-error-and-itkwidgets-error-classical-segmenter/685)
**Author:** [@jcvance](https://forum.allencell.org/u/jcvance)\ **Replies:** 0\ **Last updated:** [March 8, 2024, 4:18pm UTC](https://forum.allencell.org/t/found-way-around-not-well-formed-error-and-itkwidgets-error-classical-segmenter/685 "2024-03-08T16:18:46Z")
Hi all, I was having an issue running demo\_TNNI1 on jupyter notebook for the classical segmenter. I am running it on Windows. When reading the TNNI1 data file, I got this note: “Failed to parse XML for the provided file… --- ## [Why python, not imageJ?](https://forum.allencell.org/t/why-python-not-imagej/156)
**Author:** [@samuelorion](https://forum.allencell.org/u/samuelorion)\ **Replies:** 3\ **Last updated:** [March 1, 2024, 8:14am UTC](https://forum.allencell.org/t/why-python-not-imagej/156 "2024-03-01T08:14:15Z")
I am a relatively new user of automated image analysis methods. I am developing automated counting and tracing methods for multi well plates for primary neuronal cultures - using both standard and confocal microscopy. T… --- ## [AICSImage not Defined, Classical Segmenter](https://forum.allencell.org/t/aicsimage-not-defined-classical-segmenter/683)
**Author:** [@jcvance](https://forum.allencell.org/u/jcvance)\ **Replies:** 2\ **Last updated:** [February 27, 2024, 9:54pm UTC](https://forum.allencell.org/t/aicsimage-not-defined-classical-segmenter/683 "2024-02-27T21:54:07Z")
Hi all, I am having difficulty running playground\_npm1. After loading the image, I get this error: NameError Traceback (most recent call last) ~\\AppData\\Local\\Temp\\ipykernel\_28628\\1638… --- ## [Aicssegmentation not found in Jupyter, Classic Segmentation](https://forum.allencell.org/t/aicssegmentation-not-found-in-jupyter-classic-segmentation/681)
**Author:** [@jcvance](https://forum.allencell.org/u/jcvance)\ **Replies:** 3\ **Last updated:** [February 24, 2024, 12:11am UTC](https://forum.allencell.org/t/aicssegmentation-not-found-in-jupyter-classic-segmentation/681 "2024-02-24T00:11:31Z")
Hi, I am new to python and jupyter. I have been getting this error in demo\_TNNI1 on jupyter notebook: ModuleNotFoundError Traceback (most recent call last) ~\\AppData\\Local\\Temp\\ipykernel\_8960\\3994… --- ## [Cardiomyocyte Differentiation Issue](https://forum.allencell.org/t/cardiomyocyte-differentiation-issue/99)
**Author:** [@hwidyastuti](https://forum.allencell.org/u/hwidyastuti)\ **Replies:** 12\ **Last updated:** [February 22, 2024, 2:27pm UTC](https://forum.allencell.org/t/cardiomyocyte-differentiation-issue/99 "2024-02-22T14:27:08Z")
Hi, I’m just starting the Cardiomyocyte differentiation using the Allen Institute protocol. Currently at day 8 of differentiation and I’m starting to see some isolated beating clusters. I noticed that in the protocol the… --- ## [Commercially available, Genetically Encoded Calcium Indicator stable iPSC-cell line?](https://forum.allencell.org/t/commercially-available-genetically-encoded-calcium-indicator-stable-ipsc-cell-line/678)
**Author:** [@bkim96](https://forum.allencell.org/u/bkim96)\ **Replies:** 1\ **Last updated:** [February 9, 2024, 5:30pm UTC](https://forum.allencell.org/t/commercially-available-genetically-encoded-calcium-indicator-stable-ipsc-cell-line/678 "2024-02-09T17:30:54Z")
Our lab is looking for any commercially available Genetically encoded calcium indicator iPSC-cell lines. Could you help us to confirm if there are any of those cell lines available? Thank you for helping us! --- ## [Segmenter training data and trained models](https://forum.allencell.org/t/segmenter-training-data-and-trained-models/675)
**Author:** [@oded](https://forum.allencell.org/u/oded)\ **Replies:** 2\ **Last updated:** [January 10, 2024, 7:42pm UTC](https://forum.allencell.org/t/segmenter-training-data-and-trained-models/675 "2024-01-10T19:42:24Z")
Hi From the tutorials on segmentation I understand that there is a pipeline to be followed. First classic segmentation is done followed by DL segmentation using the good classic results as ground truth (curation). It m… --- ## [Background on sample Data](https://forum.allencell.org/t/background-on-sample-data/672)
**Author:** [@mtu2](https://forum.allencell.org/u/mtu2)\ **Replies:** 1\ **Last updated:** [December 4, 2023, 4:51pm UTC](https://forum.allencell.org/t/background-on-sample-data/672 "2023-12-04T16:51:56Z")
Hi I want to use this example dataset I got off the page on downloading cell feature data… this is the example set…I was wondering what paper its from? --- ## [Human mesenchymal stem cell culture](https://forum.allencell.org/t/human-mesenchymal-stem-cell-culture/670)
**Author:** [@Raha](https://forum.allencell.org/u/Raha)\ **Replies:** 0\ **Last updated:** [November 22, 2023, 7:57am UTC](https://forum.allencell.org/t/human-mesenchymal-stem-cell-culture/670 "2023-11-22T07:57:18Z")
Dear Friends I am new to stem cell culture. I am going to isolate human mesenchymal stem cells from fat tissue. I am not sure which medium is more suitable for these cells? DMEM high glucose, DMEM/F12, DMEM low glucose… --- ## [Cell morphology by Cell Types](https://forum.allencell.org/t/cell-morphology-by-cell-types/668)
**Author:** [@mkhisty](https://forum.allencell.org/u/mkhisty)\ **Replies:** 0\ **Last updated:** [November 21, 2023, 3:41am UTC](https://forum.allencell.org/t/cell-morphology-by-cell-types/668 "2023-11-21T03:41:45Z")
I am working on a machine learning project for which I was looking for cell morphology databases on certain types of cells (T cell, NK Cells etc.) I found this webpage from the Allen Institute: I downloaded this reso… --- ## [Differences in z-score values for the same region, same donor and same probe](https://forum.allencell.org/t/differences-in-z-score-values-for-the-same-region-same-donor-and-same-probe/666)
**Author:** [@SDH](https://forum.allencell.org/u/SDH)\ **Replies:** 0\ **Last updated:** [November 4, 2023, 5:46pm UTC](https://forum.allencell.org/t/differences-in-z-score-values-for-the-same-region-same-donor-and-same-probe/666 "2023-11-04T17:46:31Z")
I tried looking for z-scores values on Allen brain atlas (on the six healthy brain donors). Does anyone know why z-score values are different when you look at them on the two screen shots? These values are for the same … --- ## [iPS cardiac differentiation with lactate](https://forum.allencell.org/t/ips-cardiac-differentiation-with-lactate/664)
**Author:** [@hartw006](https://forum.allencell.org/u/hartw006)\ **Replies:** 1\ **Last updated:** [November 1, 2023, 9:26pm UTC](https://forum.allencell.org/t/ips-cardiac-differentiation-with-lactate/664 "2023-11-01T21:26:19Z")
Hi, Can you suggest a protocol for lactate purification after wnt-modulated differentiation? I have been unable to find a detailed protocol. thanks, Lynn --- ## [Cannot find image metadata on 'Generative Modeling with Conditional Autoencoders: Building an Integrated Cell' dataset](https://forum.allencell.org/t/cannot-find-image-metadata-on-generative-modeling-with-conditional-autoencoders-building-an-integrated-cell-dataset/662)
**Author:** [@chois](https://forum.allencell.org/u/chois)\ **Replies:** 1\ **Last updated:** [October 5, 2023, 8:41pm UTC](https://forum.allencell.org/t/cannot-find-image-metadata-on-generative-modeling-with-conditional-autoencoders-building-an-integrated-cell-dataset/662 "2023-10-05T20:41:24Z")
Hi, thank you for making available all of the beautiful datasets! I am trying to pre-process the dataset found in ‘Generative Modeling with Conditional Autoencoders: Building an Integrated Cell’ pre-print. I believe it… --- ## [Downloading Cell Feature Data](https://forum.allencell.org/t/downloading-cell-feature-data/656)
**Author:** [@mtu2](https://forum.allencell.org/u/mtu2)\ **Replies:** 10\ **Last updated:** [September 8, 2023, 7:19pm UTC](https://forum.allencell.org/t/downloading-cell-feature-data/656 "2023-09-08T19:19:46Z")
Hi I’m new here and I am looking for cell morphology data such that I have a csv where each row is a cell and each column is a shape property(eg. area, perimeter). I don’t know exactly how to search for what I need on q… --- ## [Background to Data](https://forum.allencell.org/t/background-to-data/657)
**Author:** [@mtu2](https://forum.allencell.org/u/mtu2)\ **Replies:** 0\ **Last updated:** [September 7, 2023, 7:20pm UTC](https://forum.allencell.org/t/background-to-data/657 "2023-09-07T19:20:48Z")
Hi does anyone have any background info of the example dataset posted on the page before one enter CFE? --- ## [Cannot log in to careers account](https://forum.allencell.org/t/cannot-log-in-to-careers-account/654)
**Author:** [@dgrdgr](https://forum.allencell.org/u/dgrdgr)\ **Replies:** 1\ **Last updated:** [September 4, 2023, 4:13am UTC](https://forum.allencell.org/t/cannot-log-in-to-careers-account/654 "2023-09-04T04:13:49Z")
Apologies if this is outside the scope of these forums, but I need help accessing my account on the career portal. It just tells me invalid credentials no matter how many times I reset my password. Does anyone have any … --- ## [Reason for Matrigel Concentration Recommended](https://forum.allencell.org/t/reason-for-matrigel-concentration-recommended/650)
**Author:** [@guohaodailab](https://forum.allencell.org/u/guohaodailab)\ **Replies:** 1\ **Last updated:** [August 16, 2023, 6:06pm UTC](https://forum.allencell.org/t/reason-for-matrigel-concentration-recommended/650 "2023-08-16T18:06:09Z")
Hi, we received some cells recently from your cell catalog and are in the process of thawing them. The matrigel concentration recommended (0.337 mg/mL) is a few fold higher than what is instructed by the manufacturer (C… --- ## [Defrosting in 100mm dish](https://forum.allencell.org/t/defrosting-in-100mm-dish/651)
**Author:** [@guohaodailab](https://forum.allencell.org/u/guohaodailab)\ **Replies:** 1\ **Last updated:** [August 16, 2023, 6:00pm UTC](https://forum.allencell.org/t/defrosting-in-100mm-dish/651 "2023-08-16T18:00:36Z")
Hi, We recently received cells from your catalog and noticed the directions to thaw into a 100mm dish specifically and to NOT thaw into a 6 well plate. Can you explain the decision behind this? As the cells are so valu… --- ## [Code for counting individual cells in colonies](https://forum.allencell.org/t/code-for-counting-individual-cells-in-colonies/644)
**Author:** [@guohaodailab](https://forum.allencell.org/u/guohaodailab)\ **Replies:** 1\ **Last updated:** [July 18, 2023, 6:06pm UTC](https://forum.allencell.org/t/code-for-counting-individual-cells-in-colonies/644 "2023-07-18T18:06:35Z")
Wondering if there is any available code or macro for counting individual cells in hPSC colonies? There was a method mentioned at ISSCR conference on how to get an accurate single cell count from colonies. Thanks! Stef… --- ## [Viewing cardiomyocyte scRNAseq data online?](https://forum.allencell.org/t/viewing-cardiomyocyte-scrnaseq-data-online/640)
**Author:** [@MaggietheFuqua](https://forum.allencell.org/u/MaggietheFuqua)\ **Replies:** 4\ **Last updated:** [July 6, 2023, 7:13pm UTC](https://forum.allencell.org/t/viewing-cardiomyocyte-scrnaseq-data-online/640 "2023-07-06T19:13:50Z")
Hi Allen Cell peeps! I’m wondering if there is a way to view the cardio RNAseq data (with genes and relative expression values) online? I started to do the recommended quilt option, but don’t have 400GB of free space to… --- ## [Lentivirus transduction](https://forum.allencell.org/t/lentivirus-transduction/637)
**Author:** [@en2b](https://forum.allencell.org/u/en2b)\ **Replies:** 1\ **Last updated:** [July 6, 2023, 5:19pm UTC](https://forum.allencell.org/t/lentivirus-transduction/637 "2023-07-06T17:19:10Z")
Hi there! Do you have any recommended protocols for lentiviral transduction of WTC11-dCas9-KRAB cells? I would like to make a stable knockout line. Thank you! --- ## [RNA sequences from layer 23 pyramidal neuron](https://forum.allencell.org/t/rna-sequences-from-layer-23-pyramidal-neuron/604)
**Author:** [@tom](https://forum.allencell.org/u/tom)\ **Replies:** 1\ **Last updated:** [June 24, 2023, 11:08pm UTC](https://forum.allencell.org/t/rna-sequences-from-layer-23-pyramidal-neuron/604 "2023-06-24T23:08:03Z")
If such a thing exists here or elsewhere, I was wondering if anyone can point me to a link to a web page or file of (gene name annotated if possible) expressed RNA sequences from layer 23 pyramidal neuron(s) in mice? --- ## [Targeting transcriptionally silent gene](https://forum.allencell.org/t/targeting-transcriptionally-silent-gene/633)
**Author:** [@Pratiksha](https://forum.allencell.org/u/Pratiksha)\ **Replies:** 2\ **Last updated:** [June 2, 2023, 5:58am UTC](https://forum.allencell.org/t/targeting-transcriptionally-silent-gene/633 "2023-06-02T05:58:23Z")
We have tried to target a transcriptionally silent gene with a reporter and antibiotic-resistant gene as a selection marker. We see confirmed integration of the cassette but no expression of the reporter upon differentia… --- ## [Weekend free protocols for iPS maintenance](https://forum.allencell.org/t/weekend-free-protocols-for-ips-maintenance/586)
**Author:** [@hperera](https://forum.allencell.org/u/hperera)\ **Replies:** 3\ **Last updated:** [April 20, 2023, 5:37pm UTC](https://forum.allencell.org/t/weekend-free-protocols-for-ips-maintenance/586 "2023-04-20T17:37:56Z")
Can I passage cells on a Thursday or a Friday and do a double feed on a Saturday so that I can skip a feed on a Sunday? --- ## [Antibiotic resistance in WTC derived lines?](https://forum.allencell.org/t/antibiotic-resistance-in-wtc-derived-lines/614)
**Author:** [@hartw006](https://forum.allencell.org/u/hartw006)\ **Replies:** 1\ **Last updated:** [March 9, 2023, 11:42pm UTC](https://forum.allencell.org/t/antibiotic-resistance-in-wtc-derived-lines/614 "2023-03-09T23:42:40Z")
Do any of the cell lines have antibiotic resistance genes? I am interested in using Puromycin selection --- ## [Information on dead-cas9 expressing cells](https://forum.allencell.org/t/information-on-dead-cas9-expressing-cells/301)
**Author:** [@asherypadan](https://forum.allencell.org/u/asherypadan)\ **Replies:** 3\ **Last updated:** [March 1, 2023, 10:34pm UTC](https://forum.allencell.org/t/information-on-dead-cas9-expressing-cells/301 "2023-03-01T22:34:50Z")
Please send me information on dCas9-KRAB or AICS-90 cells as well as on vectors expressing dCas. We seek viral vectors and/or expressing iPSC. Thank you in advance, Ruth --- ## [sgRNA transfection](https://forum.allencell.org/t/sgrna-transfection/603)
**Author:** [@en2b](https://forum.allencell.org/u/en2b)\ **Replies:** 0\ **Last updated:** [January 23, 2023, 8:01pm UTC](https://forum.allencell.org/t/sgrna-transfection/603 "2023-01-23T20:01:20Z")
I am planning to transfect the WTC11-dCas9-KRAB cell line with sgRNA for gene knockdown. Do you have a recommended amount of sgRNA to transfect when the cells are already expressing dCas9? --- ## [Cryo-preserving in CryoStor?](https://forum.allencell.org/t/cryo-preserving-in-cryostor/596)
**Author:** [@OBEID](https://forum.allencell.org/u/OBEID)\ **Replies:** 2\ **Last updated:** [January 20, 2023, 4:00am UTC](https://forum.allencell.org/t/cryo-preserving-in-cryostor/596 "2023-01-20T04:00:25Z")
I would like to know if i can cryo-preserve my cell line (AISC-0012) in CryoStorCS10 from StemCell Technologies (#07959). Thank you Pat --- ## [Dilution of Matrigel : which media?](https://forum.allencell.org/t/dilution-of-matrigel-which-media/595)
**Author:** [@OBEID](https://forum.allencell.org/u/OBEID)\ **Replies:** 2\ **Last updated:** [January 19, 2023, 5:10am UTC](https://forum.allencell.org/t/dilution-of-matrigel-which-media/595 "2023-01-19T05:10:07Z")
I have a doubt… In the protocol version 1.7, I read that you have to dilute the Matrigel in DMEM/F12 to make the coating. But in paragraph 13 of the Passaging section, I understand that the Matrigel is prepared in mTeSR… --- ## [Can I use Glutamax versions of media and still get good differentiation to cardiac?](https://forum.allencell.org/t/can-i-use-glutamax-versions-of-media-and-still-get-good-differentiation-to-cardiac/580)
**Author:** [@hartw006](https://forum.allencell.org/u/hartw006)\ **Replies:** 1\ **Last updated:** [January 5, 2023, 6:55pm UTC](https://forum.allencell.org/t/can-i-use-glutamax-versions-of-media-and-still-get-good-differentiation-to-cardiac/580 "2023-01-05T18:55:07Z")
Can I use RPMI with glutamax (also other versions with glutamine replaced with di peptide- Ala-Gln) and still have good differentiation to cardiac? I assume that mTesr1 Plus is similarly a replacement of glutamax for g… [Previous page](https://forum.allencell.org/latest.md) [Next page](https://forum.allencell.org/latest.md?page=2)