Merge pull request #3 from fish-quant/dev

Finalize

.github/workflows/python-publish.yml

@@ -3,7 +3,10 @@
 
 name: Upload Python Package
 
-on: push
+on:
+  push:
+    branches:
+      - main
 
 jobs:
   build-n-publish:

README.md

@@ -1,4 +1,7 @@
-# Automator
+![GitHub](https://img.shields.io/github/license/fish-quant/autofish)
+[![Python 3.7](https://img.shields.io/badge/python-3.7-blue.svg)](https://www.python.org/downloads/release/python-390/)
+
+# autoFISH - automated FISH experiments
 
 Python library to control an automated fluidics system and perform microscope acquisition for iterative FISH experiments.
 
@@ -13,15 +16,27 @@ See dedicated documentation [**here**](https://github.com/fish-quant/autofish/bl
 ### Installation
 
 1. Download latest version of miniconda from [**here**](https://docs.conda.io/en/latest/miniconda.html) (can also be Python 3.X).
-2. Open Anaconda terminal and create dedicated environment: `conda create --name autofish python=3.7`
+2. Open Anaconda terminal and create dedicated environment: `conda create --name autofish python=3.9`
 3. Activate environment: `conda activate autofish`
-4. Pip install `pip install -i https://test.pypi.org/simple/ autofish==0.0.1`
+4. Pip install `pip install -i https://test.pypi.org/simple/ autofish`
 
 ### Starting autofish
 
 1. Open Anaconda terminal and activate environment: `conda activate autofish`
 2. Start user interface with command `autofish`
 
+### Configuration files
+
+The behavior of the fluidics and acquistion system is defined by several config files.
+
+* To test the installation of autofish, you can use demo configurations which require neither a microscope nor a fluidics systems: <https://github.com/fish-quant/autofish/tree/main/demo>
+
+* We provide config files that we use on our system (with a Nikon Ti): <https://github.com/fish-quant/autofish/tree/main/configs>
+
 ### Building the Fluidics system
 
 See dedicated documentation [**here**](https://github.com/fish-quant/autofish/blob/master/docs/fluidics_construction.pdf) for how to build the fluidics system.
+
+## Reporting a problem/suggestion
+
+If you encounter a problem or you have a suggestion, please file an [**issue**](https://github.com/fish-quant/autofish/issues).

configs/_file_sync.txt

@@ -0,0 +1 @@
+0

configs/experiment_config__seqFISH-CLASSIC-SABER.yaml

@@ -0,0 +1,92 @@
+#Different buffers: stored as a list [valve-id,cnc-plate,cnc-well or position ]
+buffers:
+    wash_SABER_v3: [3,null,null]
+    wash_v4: [4,null,null]
+    image_v5: [5,null,null]
+
+    clean_plate: [6,1,A1]
+    prime_plate: [6,1,A2]
+
+    dapi_r1: [6,1,A3]
+    w_r1: [6,1,A4]
+    h_r1: [6,1,A5]
+
+    w_r2: [6,1,A6]
+    h_r2: [6,1,A7]
+
+    w_r3: [6,1,A8]
+    h_r3: [6,1,A9]
+
+    w_r4: [6,1,A10]
+    h_r4: [6,1,A11]
+
+    w_r5: [6,1,A12]
+    h_r5: [6,1,B1]
+    SAB_w_r5: [6,1,B2]
+    SAB_h_IM_r5: [6,1,B3]   
+
+    w_r6: [6,1,B4]
+    h_r6: [6,1,B5]
+    SAB_w_r6: [6,1,B6]
+    SAB_h_IM_r6: [6,1,B7]   
+
+    w_r7: [6,1,B8]
+    h_r7: [6,1,B9]
+    SAB_w_r7: [6,1,B10]
+    SAB_h_IM_r7: [6,1,B11]   
+
+    w_r8: [6,1,B12]
+    h_r8: [6,1,C1]
+    SAB_w_r8: [6,1,C2]
+    SAB_h_IM_r8: [6,1,C3]   
+
+
+# Sequence of a given fluidic run. Possible actions and parameters are "buffer": buffers listed in buffer_config.yaml, ii will be looped over; pump: time for pumping [s], pause: time for pause [s], image: 1.
+sequence:
+    - buffer: w_ii
+    - pump: 180
+    - buffer: h_ii
+    - pump: 180
+    - pause: 1200
+    - buffer: wash_v4
+    - pump: 180
+    - pause: 180
+    - - round: r1
+      - buffer: dapi_ii
+      - pump: 180
+      - pause: 180
+      - buffer: wash_v4
+      - pump: 180
+      - pause: 60  
+    - pump: 180
+    - pause: 180
+    - - round: r5,r6,r7,r8
+      - buffer: SAB_w_ii
+      - pump: 180
+      - pause: 180
+      - buffer: SAB_h_IM_ii  
+      - pump: 180
+      - pause: 1200
+      - buffer: wash_SABER_v3
+      - pump: 180
+      - pause: 180
+      - buffer: wash_SABER_v3
+      - pump: 180
+      - pause: 180
+    - buffer: image_v5
+    - pump: 180  
+    - pause: 120      
+
+#Well plate setup: once calibrated, you usuall don't have to change this
+well_plate:
+    top_right:
+      x: 63
+      y: 99
+    bottom_left:
+      x: 0
+      y: 0
+    columns: 8
+    rows: 12
+    well_spacing: 9
+    z_base: -37
+    feed: 500

configs/experiment_config__seqFISH-DAPI.yaml

@@ -0,0 +1,98 @@
+#Different buffers: stored as a list [valve-id,cnc-plate,cnc-well or position ]
+buffers:
+    wash_valve4: [4,null,null]
+    wash_SSC_valve5: [5,null,null]
+    image_valve6: [6,null,null]
+    clean_plate: [6,1,A1]
+    prime_plate: [6,1,A2]
+    dapi_r1: [6,1,A3]
+    w_r1: [6,1,A4]
+    h_r1: [6,1,A5]
+    w_r2: [6,1,A6]
+    h_r2: [6,1,A7]
+    w_r3: [6,1,A8]
+    h_r3: [6,1,A9]
+    w_r4: [6,1,A10]
+    h_r4: [6,1,A11]
+    w_r5: [6,1,A12]
+    h_r5: [6,1,B1]
+    w_r6: [6,1,B2]
+    h_r6: [6,1,B3]
+    w_r7: [6,1,B4]
+    h_r7: [6,1,B5]
+    w_r8: [6,1,B6]
+    h_r8: [6,1,B7]  
+    w_r9: [6,1,B8]
+    h_r9: [6,1,B9]   
+    w_r10: [6,1,B10]
+    h_r10: [6,1,B11]
+    w_r11: [6,1,B12]
+    h_r11: [6,1,C1]   
+    w_r12: [6,1,C2]
+    h_r12: [6,1,C3]
+    w_r13: [6,1,C4]
+    h_r13: [6,1,C5]
+    w_r14: [6,1,C6]
+    h_r14: [6,1,C7]
+    w_r15: [6,1,C8]
+    h_r15: [6,1,C9]
+    w_r16: [6,1,C10]
+    h_r16: [6,1,C11]
+    w_r17: [6,1,C12]
+    h_r17: [6,1,D1]
+    w_r18: [6,1,D2]
+    h_r18: [6,1,D3]  
+    w_r19: [6,1,D4]
+    h_r19: [6,1,D5]  
+    w_r20: [6,1,D6]
+    h_r20: [6,1,D7]  
+
+
+# Sequence of a given fluidic run. Possible actions and parameters are "buffer": buffers listed in buffer_config.yaml, ii will be looped over; pump: time for pumping [s], pause: time for pause [s], image: 1.
+sequence:
+    - buffer: wash_SSC_valve5
+    - pump: 180
+    - pause: 60
+    - buffer: w_ii
+    - pump: 180
+    - buffer: h_ii
+    - pump: 180
+    - pause: 1800
+    - buffer: wash_valve4
+    - pump: 180
+    - pause: 60
+    - - round: r1
+      - buffer: dapi_ii
+      - pump: 180
+      - pause: 180
+      - buffer: wash_valve4
+      - pump: 180
+      - pause: 60 
+    - pump: 180
+    - pause: 60    
+    - buffer: wash_SSC_valve5
+    - pump: 180
+    - pause: 60
+    - buffer: image_valve6
+    - pump: 180  
+    - pause: 120     
+    - image: 1    
+
+#Well plate setup: once calibrated, you usuall don't have to change this
+well_plate:
+    top_right:
+      x: 63
+      y: 99
+    bottom_left:
+      x: 0
+      y: 0
+    columns: 8
+    rows: 12
+    well_spacing: 9
+    z_base: -37
+    feed: 500
+
+
+
+
+

configs/microscope_config__NikonTi_Cy3-Cy5-DAPI.yaml

@@ -0,0 +1,14 @@
+microscope:
+    type: 'NIKON_TI'
+    timeout: 5000
+    xy_drive_name: 'TIXYDrive'
+    z_drive_name: 'TIPFSOffset'
+    channel_group: 'Channel'
+    channels: ['Cy3_75', 'Cy5_50','Dapi_50']
+    channel_blank: Cy3_0
+    channel_exposures_ms: [300,50,100]
+    z_start: -15
+    z_end: 60
+    z_step: 2.5
+    mm_app_path: 'C:\Program Files\Micro-Manager-2.0-nightly'
+    mm_config_file: 'Zstack_with_PFS.cfg'

configs/microscope_config__NikonTi_Cy3-Cy5.yaml

@@ -0,0 +1,14 @@
+microscope:
+    type: 'NIKON_TI'
+    timeout: 5000
+    xy_drive_name: 'TIXYDrive'
+    z_drive_name: 'TIPFSOffset'
+    channel_group: 'Channel'
+    channels: ['Cy3_75', 'Cy5_50']
+    channel_blank: Cy3_0
+    channel_exposures_ms: [300,50]
+    z_start: -15
+    z_end: 60
+    z_step: 2.5
+    mm_app_path: 'C:\Program Files\Micro-Manager-2.0-nightly'
+    mm_config_file: 'Zstack_with_PFS.cfg'

configs/system_config.json

@@ -0,0 +1,32 @@
+{
+    "pump": {
+        "test_command": "1#\r",
+        "response": "REGLO DIGITAL",
+        "type": "REGLO DIGITAL",
+        "baudrate": 9600,
+        "COM": "COM8",
+        "Revolution": "CCW",
+        "Flowrate": 0.5
+    },
+    "valve": {
+        "test_command": "/1h30001R\r",
+        "response": "/0",
+        "type": "HAMILTON MVP",
+        "baudrate": 9600,
+        "COM": "COM7"
+    },
+    "plate": {
+        "wake_up": "\r\n\r\n",
+        "test_command": "$I\n",
+        "response": "VER:",
+        "type": "CNCRouter3018PRO",
+        "baudrate": 115200,
+        "COM": "COM11"
+    },
+    "flow_sensor": {
+        "type": "Sensirion_csv",
+        "log_file": "C:\\Temp\\DataLog.csv",
+        "kernel_size": 20,
+        "flow_min": 20
+    }
+}